SMTL ID : 3owm.1

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 25 residues within 4Å: Chain A: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, V.179, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.3, NO2.9 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.112, A:V.125, A:A.128, A:V.297, A:Y.299, A:Y.299, A:Y.299, A:F.323 Hydrogen bonds: A:A.110, A:A.480, A:N.482 Water bridges: A:H.109, A:H.109, A:H.109, A:R.127, A:H.357 Salt bridges: A:K.86, A:H.109, A:H.109, A:R.127, A:H.357 pi-Stacking: A:H.357 Metal complexes: H2O.23 HEC.2: 19 residues within 4Å: Chain A: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.3, HEC.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.66, A:Q.69, A:F.73, A:L.221, A:A.286, A:T.392 Hydrogen bonds: A:Q.69, A:T.392, A:T.392 Salt bridges: A:K.382 Metal complexes: A:H.227, A:H.394 HEC.3: 26 residues within 4Å: Chain A: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.1, HEC.2, HEC.4, CA.11 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:P.112, A:H.379, A:Q.396 Hydrogen bonds: A:S.80, A:R.113, A:F.117, A:D.121 Water bridges: A:R.77, A:R.77, A:R.77, A:H.122 Metal complexes: A:H.115, A:H.296 HEC.4: 24 residues within 4Å: Chain A: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.3, HEC.5, CA.11 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:H.296, A:E.359, A:E.359, A:F.363, A:H.368, A:V.373, A:P.399, A:I.423, A:N.482, A:F.486, A:F.486 Hydrogen bonds: A:T.398, A:T.398 Water bridges: A:R.77, A:S.80, A:K.427, A:N.482 Salt bridges: A:R.400, A:K.427 Metal complexes: A:H.379, A:H.487 HEC.5: 18 residues within 4Å: Chain A: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Chain C: N.137, W.138, Q.139 Ligands: HEC.4, PG4.21 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.367, A:N.371, A:V.373, A:P.399, A:W.414, A:I.423, A:F.486, C:Q.139 Water bridges: A:N.371, C:Q.139 Metal complexes: A:H.368, A:H.411 Hydrogen bonds: C:W.138 HEC.6: 23 residues within 4Å: Chain A: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.7, HEC.8 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:A.7, A:F.11, A:I.17, A:I.17, A:V.29, A:T.55, A:I.189, A:L.190, A:F.224, A:P.229, A:F.270 Water bridges: A:R.278 Salt bridges: A:R.235, A:R.272, A:R.278, A:R.278 Metal complexes: A:H.35, A:H.230 HEC.7: 17 residues within 4Å: Chain A: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Chain B: H.33, T.64, C.65 Ligands: HEC.2, HEC.6 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:K.25, A:K.25, A:H.227, A:A.232, B:T.64 Hydrogen bonds: A:A.232 Water bridges: A:K.25 Salt bridges: A:K.25, A:K.25 Metal complexes: A:H.26, A:H.66 HEC.8: 23 residues within 4Å: Chain A: V.5, Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272, G.273 Ligands: HEC.6 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:V.5, A:A.37, A:V.41, A:M.49, A:P.53 Hydrogen bonds: A:G.273 Water bridges: A:R.272, A:R.272 Salt bridges: A:R.52, A:R.272, A:R.272 Metal complexes: A:H.14, A:H.40 HEC.24: 24 residues within 4Å: Chain B: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.26, NO2.32 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.112, B:V.125, B:A.128, B:V.297, B:Y.299, B:Y.299, B:F.323, B:H.357 Hydrogen bonds: B:A.110, B:A.480, B:N.482 Water bridges: B:R.127, B:H.357 Salt bridges: B:K.86, B:H.109, B:R.127, B:H.357 pi-Stacking: B:Y.299, B:H.357 Metal complexes: H2O.48 HEC.25: 18 residues within 4Å: Chain B: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.26, HEC.30 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:H.66, B:Q.69, B:F.73, B:L.221, B:A.286, B:T.392 Hydrogen bonds: B:Q.69, B:T.392 Metal complexes: B:H.227, B:H.394 HEC.26: 26 residues within 4Å: Chain B: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.24, HEC.25, HEC.27, CA.34 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:P.112, B:K.184, B:L.221, B:H.379, B:Q.396, B:Q.396 Hydrogen bonds: B:S.80, B:F.117 Water bridges: B:R.77, B:R.77, B:R.77, B:H.122, B:Q.396 Metal complexes: B:H.115, B:H.296 HEC.27: 24 residues within 4Å: Chain B: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.26, HEC.28, CA.34 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:H.296, B:E.359, B:E.359, B:F.363, B:H.368, B:V.373, B:P.399, B:I.423, B:N.482, B:F.486, B:F.486 Hydrogen bonds: B:T.398 Water bridges: B:R.77, B:S.80, B:K.427, B:N.482 Salt bridges: B:R.400, B:K.427 Metal complexes: B:H.379, B:H.487 HEC.28: 19 residues within 4Å: Chain B: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Chain F: N.137, W.138, Q.139 Ligands: HEC.27, PG4.46 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain F, Hydrophobic interactions: B:V.367, B:P.399, B:W.414, B:I.423, B:F.486, F:W.138, F:Q.139 Water bridges: B:N.371, F:Q.139 Metal complexes: B:H.368, B:H.411 Hydrogen bonds: F:W.138, F:Q.139 HEC.29: 23 residues within 4Å: Chain B: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.30, HEC.31 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.7, B:F.11, B:I.17, B:I.17, B:V.29, B:T.55, B:I.189, B:L.190, B:F.224, B:P.229, B:F.270 Water bridges: B:R.278 Salt bridges: B:R.235, B:R.272, B:R.278, B:R.278 Metal complexes: B:H.35, B:H.230 HEC.30: 16 residues within 4Å: Chain A: H.33, C.65 Chain B: K.25, H.26, V.29, H.33, A.61, C.62, C.65, H.66, C.223, H.227, A.232 Ligands: NA.23, HEC.25, HEC.29 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:K.25, B:K.25, B:H.227, B:A.232 Water bridges: B:K.25 Salt bridges: B:K.25, B:K.25 Metal complexes: B:H.26, B:H.66 HEC.31: 22 residues within 4Å: Chain B: Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.47, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272 Ligands: HEC.29 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:A.37, B:V.41, B:M.49, B:P.53 Water bridges: B:H.14, B:Q.271, B:R.272, B:R.272 Salt bridges: B:H.14, B:R.52, B:R.272 Metal complexes: B:H.14, B:H.40 HEC.47: 25 residues within 4Å: Chain C: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, V.179, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.49, NO2.55 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:P.112, C:V.125, C:A.128, C:V.297, C:Y.299, C:Y.299, C:Y.299, C:F.323 Hydrogen bonds: C:A.110, C:A.480, C:N.482 Water bridges: C:H.109, C:A.110, C:R.127, C:H.357 Salt bridges: C:K.86, C:H.109, C:H.109, C:R.127, C:H.357 pi-Stacking: C:H.357 Metal complexes: H2O.71 HEC.48: 19 residues within 4Å: Chain C: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.49, HEC.53 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:H.66, C:Q.69, C:F.73, C:L.221, C:A.286, C:T.392 Hydrogen bonds: C:Q.69, C:T.392, C:T.392 Salt bridges: C:K.382 Metal complexes: C:H.227, C:H.394 HEC.49: 26 residues within 4Å: Chain C: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.47, HEC.48, HEC.50, CA.57 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:P.112, C:H.379, C:Q.396 Hydrogen bonds: C:S.80, C:P.112, C:R.113, C:F.117 Water bridges: C:R.77, C:R.77, C:R.77, C:H.122 Metal complexes: C:H.115, C:H.296 HEC.50: 24 residues within 4Å: Chain C: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.49, HEC.51, CA.57 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:H.296, C:E.359, C:E.359, C:F.363, C:H.368, C:V.373, C:P.399, C:I.423, C:N.482, C:F.486, C:F.486 Hydrogen bonds: C:T.398, C:T.398 Water bridges: C:R.77, C:S.80, C:K.427, C:N.482 Salt bridges: C:R.400, C:K.427 Metal complexes: C:H.379, C:H.487 HEC.51: 18 residues within 4Å: Chain C: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Chain E: N.137, W.138, Q.139 Ligands: HEC.50, PG4.67 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:V.367, C:N.371, C:V.373, C:P.399, C:W.414, C:I.423, C:F.486, E:Q.139 Water bridges: C:N.371, E:Q.139 Metal complexes: C:H.368, C:H.411 Hydrogen bonds: E:W.138 HEC.52: 23 residues within 4Å: Chain C: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.53, HEC.54 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:A.7, C:F.11, C:I.17, C:I.17, C:V.29, C:T.55, C:I.189, C:L.190, C:F.224, C:P.229, C:F.270 Water bridges: C:R.278 Salt bridges: C:R.235, C:R.272, C:R.278, C:R.278 Metal complexes: C:H.35, C:H.230 HEC.53: 17 residues within 4Å: Chain C: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Chain D: H.33, T.64, C.65 Ligands: HEC.48, HEC.52 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D, Hydrophobic interactions: C:K.25, C:K.25, C:H.227, C:A.232, D:T.64 Hydrogen bonds: C:A.232 Water bridges: C:K.25, D:T.64 Salt bridges: C:K.25, C:K.25 Metal complexes: C:H.26, C:H.66 HEC.54: 23 residues within 4Å: Chain C: V.5, Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272, G.273 Ligands: HEC.52 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:V.5, C:A.37, C:V.41, C:M.49, C:P.53 Hydrogen bonds: C:G.273 Water bridges: C:R.272, C:R.272 Salt bridges: C:R.52, C:R.272, C:R.272 Metal complexes: C:H.14, C:H.40 HEC.70: 24 residues within 4Å: Chain D: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.72, NO2.78 20 PLIP interactions: 19 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:P.112, D:V.125, D:A.128, D:V.297, D:Y.299, D:Y.299, D:F.323, D:H.357 Hydrogen bonds: D:A.110, D:A.480, D:N.482 Water bridges: D:R.127, D:H.357 Salt bridges: D:K.86, D:H.109, D:R.127, D:H.357 pi-Stacking: D:Y.299, D:H.357 Metal complexes: H2O.96 HEC.71: 18 residues within 4Å: Chain D: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.72, HEC.76 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:H.66, D:Q.69, D:F.73, D:L.221, D:A.286, D:T.392 Hydrogen bonds: D:Q.69, D:T.392 Metal complexes: D:H.227, D:H.394 HEC.72: 26 residues within 4Å: Chain D: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.70, HEC.71, HEC.73, CA.80 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:P.112, D:K.184, D:L.221, D:H.379, D:Q.396, D:Q.396 Hydrogen bonds: D:S.80, D:R.113, D:F.117, D:D.121 Water bridges: D:R.77, D:R.77, D:R.77, D:H.122, D:Q.396 Metal complexes: D:H.115, D:H.296 HEC.73: 24 residues within 4Å: Chain D: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.72, HEC.74, CA.80 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:H.296, D:E.359, D:E.359, D:F.363, D:H.368, D:V.373, D:P.399, D:I.423, D:N.482, D:F.486, D:F.486 Hydrogen bonds: D:T.398, D:T.398 Water bridges: D:R.77, D:S.80, D:K.427, D:N.482 Salt bridges: D:R.400, D:K.427 Metal complexes: D:H.379, D:H.487 HEC.74: 19 residues within 4Å: Chain B: N.137, W.138, Q.139 Chain D: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Ligands: HEC.73, PG4.92 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain D, Hydrophobic interactions: B:W.138, B:Q.139, D:V.367, D:P.399, D:W.414, D:I.423, D:F.486 Hydrogen bonds: B:W.138, B:Q.139 Water bridges: B:Q.139, D:N.371 Metal complexes: D:H.368, D:H.411 HEC.75: 23 residues within 4Å: Chain D: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.76, HEC.77 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:A.7, D:F.11, D:I.17, D:I.17, D:V.29, D:T.55, D:I.189, D:L.190, D:F.224, D:P.229, D:F.270 Water bridges: D:R.278 Salt bridges: D:R.235, D:R.272, D:R.278, D:R.278 Metal complexes: D:H.35, D:H.230 HEC.76: 16 residues within 4Å: Chain C: H.33, C.65 Chain D: K.25, H.26, V.29, H.33, A.61, C.62, C.65, H.66, C.223, H.227, A.232 Ligands: NA.69, HEC.71, HEC.75 9 PLIP interactions: 9 interactions with chain D, Hydrophobic interactions: D:K.25, D:K.25, D:H.227, D:A.232 Water bridges: D:K.25 Salt bridges: D:K.25, D:K.25 Metal complexes: D:H.26, D:H.66 HEC.77: 22 residues within 4Å: Chain D: Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.47, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272 Ligands: HEC.75 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:A.37, D:V.41, D:M.49, D:P.53 Water bridges: D:H.14, D:Q.271, D:R.272, D:R.272 Salt bridges: D:H.14, D:R.52, D:R.272 Metal complexes: D:H.14, D:H.40 HEC.93: 25 residues within 4Å: Chain E: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, V.179, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.95, NO2.101 23 PLIP interactions: 22 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:P.112, E:V.125, E:A.128, E:V.297, E:Y.299, E:Y.299, E:Y.299, E:F.323 Hydrogen bonds: E:A.110, E:A.480, E:N.482 Water bridges: E:H.109, E:H.109, E:H.109, E:R.127, E:H.357 Salt bridges: E:K.86, E:H.109, E:H.109, E:R.127, E:H.357 pi-Stacking: E:H.357 Metal complexes: H2O.119 HEC.94: 19 residues within 4Å: Chain E: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.95, HEC.99 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:H.66, E:Q.69, E:F.73, E:L.221, E:A.286, E:T.392 Hydrogen bonds: E:Q.69, E:T.392, E:T.392 Salt bridges: E:K.382 Metal complexes: E:H.227, E:H.394 HEC.95: 26 residues within 4Å: Chain E: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.93, HEC.94, HEC.96, CA.103 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:P.112, E:H.379, E:Q.396 Hydrogen bonds: E:S.80, E:P.112, E:R.113, E:F.117 Water bridges: E:R.77, E:R.77, E:R.77, E:H.122 Metal complexes: E:H.115, E:H.296 HEC.96: 24 residues within 4Å: Chain E: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.95, HEC.97, CA.103 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:H.296, E:E.359, E:E.359, E:F.363, E:H.368, E:V.373, E:P.399, E:I.423, E:N.482, E:F.486, E:F.486 Hydrogen bonds: E:T.398 Water bridges: E:R.77, E:S.80, E:K.427, E:N.482 Salt bridges: E:R.400, E:K.427 Metal complexes: E:H.379, E:H.487 HEC.97: 18 residues within 4Å: Chain A: N.137, W.138, Q.139 Chain E: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Ligands: HEC.96, PG4.113 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.367, E:N.371, E:V.373, E:P.399, E:W.414, E:I.423, E:F.486, A:Q.139 Water bridges: E:N.371, A:Q.139 Metal complexes: E:H.368, E:H.411 Hydrogen bonds: A:W.138 HEC.98: 23 residues within 4Å: Chain E: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.99, HEC.100 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:A.7, E:F.11, E:I.17, E:I.17, E:V.29, E:T.55, E:I.189, E:L.190, E:F.224, E:P.229, E:F.270 Water bridges: E:R.278 Salt bridges: E:R.235, E:R.272, E:R.278, E:R.278 Metal complexes: E:H.35, E:H.230 HEC.99: 17 residues within 4Å: Chain E: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Chain F: H.33, T.64, C.65 Ligands: HEC.94, HEC.98 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain F, Hydrophobic interactions: E:K.25, E:K.25, E:H.227, E:A.232, F:T.64 Hydrogen bonds: E:A.232 Water bridges: E:K.25, F:T.64 Salt bridges: E:K.25, E:K.25 Metal complexes: E:H.26, E:H.66 HEC.100: 23 residues within 4Å: Chain E: V.5, Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272, G.273 Ligands: HEC.98 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:V.5, E:A.37, E:V.41, E:M.49, E:P.53 Hydrogen bonds: E:G.273 Water bridges: E:R.272, E:R.272 Salt bridges: E:R.52, E:R.272, E:R.272 Metal complexes: E:H.14, E:H.40 HEC.116: 24 residues within 4Å: Chain F: H.109, A.110, P.112, D.121, H.122, V.125, R.127, A.128, A.175, C.180, C.183, K.184, R.238, C.295, H.296, V.297, Y.299, C.301, F.323, H.357, A.480, N.482 Ligands: HEC.118, NO2.124 21 PLIP interactions: 20 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:P.112, F:V.125, F:A.128, F:V.297, F:Y.299, F:Y.299, F:F.323, F:H.357 Hydrogen bonds: F:A.110, F:A.480, F:N.482 Water bridges: F:H.109, F:R.127, F:H.357 Salt bridges: F:K.86, F:H.109, F:R.127, F:H.357 pi-Stacking: F:Y.299, F:H.357 Metal complexes: H2O.144 HEC.117: 18 residues within 4Å: Chain F: C.62, H.66, Q.69, F.70, F.73, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.118, HEC.122 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:H.66, F:Q.69, F:F.73, F:L.221, F:A.286, F:T.392 Hydrogen bonds: F:Q.69, F:T.392 Metal complexes: F:H.227, F:H.394 HEC.118: 26 residues within 4Å: Chain F: R.77, S.80, P.112, R.113, S.114, H.115, F.117, M.118, D.121, C.183, K.184, L.221, M.225, M.291, C.292, C.295, H.296, C.375, H.379, M.380, Q.396, R.397 Ligands: HEC.116, HEC.117, HEC.119, CA.126 17 PLIP interactions: 17 interactions with chain F, Hydrophobic interactions: F:P.112, F:K.184, F:L.221, F:H.379, F:Q.396, F:Q.396 Hydrogen bonds: F:S.80, F:R.113, F:F.117, F:D.121 Water bridges: F:R.77, F:R.77, F:R.77, F:H.122, F:Q.396 Metal complexes: F:H.115, F:H.296 HEC.119: 24 residues within 4Å: Chain F: N.289, C.292, H.296, E.359, A.360, F.363, H.368, V.373, A.374, C.375, C.378, H.379, T.398, P.399, R.400, I.423, K.427, N.482, S.483, F.486, H.487 Ligands: HEC.118, HEC.120, CA.126 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:H.296, F:E.359, F:E.359, F:F.363, F:H.368, F:V.373, F:P.399, F:I.423, F:N.482, F:F.486, F:F.486 Hydrogen bonds: F:T.398 Water bridges: F:R.77, F:S.80, F:K.427, F:N.482 Salt bridges: F:R.400, F:K.427 Metal complexes: F:H.379, F:H.487 HEC.120: 19 residues within 4Å: Chain D: N.137, W.138, Q.139 Chain F: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, I.423, F.486 Ligands: HEC.119, PG4.138 13 PLIP interactions: 8 interactions with chain F, 5 interactions with chain D, Hydrophobic interactions: F:V.367, F:P.399, F:W.414, F:I.423, F:F.486, D:W.138, D:Q.139 Water bridges: F:N.371, D:Q.139 Metal complexes: F:H.368, F:H.411 Hydrogen bonds: D:W.138, D:Q.139 HEC.121: 23 residues within 4Å: Chain F: A.7, C.10, F.11, H.14, I.17, H.21, V.29, N.30, C.31, C.34, H.35, T.55, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.122, HEC.123 18 PLIP interactions: 18 interactions with chain F, Hydrophobic interactions: F:A.7, F:F.11, F:I.17, F:I.17, F:V.29, F:T.55, F:I.189, F:L.190, F:F.224, F:P.229, F:F.270 Water bridges: F:R.278 Salt bridges: F:R.235, F:R.272, F:R.278, F:R.278 Metal complexes: F:H.35, F:H.230 HEC.122: 16 residues within 4Å: Chain E: H.33, C.65 Chain F: K.25, H.26, V.29, H.33, A.61, C.62, C.65, H.66, C.223, H.227, A.232 Ligands: NA.115, HEC.117, HEC.121 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:K.25, F:K.25, F:H.227, F:A.232 Water bridges: F:K.25 Salt bridges: F:K.25, F:K.25 Metal complexes: F:H.26, F:H.66 HEC.123: 22 residues within 4Å: Chain F: Q.9, C.10, C.13, H.14, C.31, H.35, A.37, H.40, V.41, A.44, S.45, S.46, R.47, R.48, M.49, R.52, P.53, T.55, L.190, Q.271, R.272 Ligands: HEC.121 13 PLIP interactions: 13 interactions with chain F, Hydrophobic interactions: F:A.37, F:V.41, F:M.49, F:P.53 Water bridges: F:H.14, F:Q.271, F:R.272, F:R.272 Salt bridges: F:H.14, F:R.52, F:R.272 Metal complexes: F:H.14, F:H.40

6 x NO2: NITRITE ION(Non-covalent)

NO2.9: 5 residues within 4Å: Chain A: K.184, Y.299, Q.356, H.357 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.127, A:R.127, A:Y.299 NO2.32: 5 residues within 4Å: Chain B: K.184, Y.299, Q.356, H.357 Ligands: HEC.24 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.184, B:Y.299 Water bridges: B:R.127, B:R.127, B:R.127 NO2.55: 5 residues within 4Å: Chain C: K.184, Y.299, Q.356, H.357 Ligands: HEC.47 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.184, C:Y.299 Water bridges: C:R.127, C:R.127, C:R.127 NO2.78: 5 residues within 4Å: Chain D: K.184, Y.299, Q.356, H.357 Ligands: HEC.70 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.184 Water bridges: D:R.127, D:R.127, D:Y.299 NO2.101: 5 residues within 4Å: Chain E: K.184, Y.299, Q.356, H.357 Ligands: HEC.93 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.184, E:Y.299 Water bridges: E:R.127, E:R.127, E:R.127 NO2.124: 5 residues within 4Å: Chain F: K.184, Y.299, Q.356, H.357 Ligands: HEC.116 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.184 Water bridges: F:R.127, F:R.127, F:Y.299

18 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.10: 4 residues within 4Å: Chain A: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.298, A:Y.299, A:K.354, H2O.14, H2O.14 CA.11: 4 residues within 4Å: Chain A: S.80, P.112 Ligands: HEC.3, HEC.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.112, H2O.5, H2O.5, H2O.21 CA.13: 2 residues within 4Å: Ligands: CA.59, CA.105 No protein-ligand interaction detected (PLIP) CA.33: 4 residues within 4Å: Chain B: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.298, B:Y.299, B:K.354, H2O.39, H2O.39 CA.34: 3 residues within 4Å: Chain B: P.112 Ligands: HEC.26, HEC.27 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:P.112, H2O.27, H2O.27, H2O.46 CA.36: 2 residues within 4Å: Ligands: CA.82, CA.128 No protein-ligand interaction detected (PLIP) CA.56: 4 residues within 4Å: Chain C: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.298, C:Y.299, C:K.354, H2O.62, H2O.62 CA.57: 4 residues within 4Å: Chain C: S.80, P.112 Ligands: HEC.49, HEC.50 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:P.112, H2O.53, H2O.53, H2O.69 CA.59: 2 residues within 4Å: Ligands: CA.13, CA.105 No protein-ligand interaction detected (PLIP) CA.79: 4 residues within 4Å: Chain D: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.298, D:Y.299, D:K.354, H2O.87, H2O.87 CA.80: 3 residues within 4Å: Chain D: P.112 Ligands: HEC.72, HEC.73 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:P.112, H2O.74, H2O.75, H2O.94 CA.82: 2 residues within 4Å: Ligands: CA.36, CA.128 No protein-ligand interaction detected (PLIP) CA.102: 4 residues within 4Å: Chain E: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.298, E:Y.299, E:K.354, H2O.109, H2O.109 CA.103: 4 residues within 4Å: Chain E: S.80, P.112 Ligands: HEC.95, HEC.96 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:P.112, H2O.100, H2O.101, H2O.117 CA.105: 2 residues within 4Å: Ligands: CA.13, CA.59 No protein-ligand interaction detected (PLIP) CA.125: 4 residues within 4Å: Chain F: E.298, Y.299, K.354, Q.356 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.298, F:Y.299, F:K.354, H2O.134, H2O.135 CA.126: 3 residues within 4Å: Chain F: P.112 Ligands: HEC.118, HEC.119 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:P.112, H2O.122, H2O.122, H2O.142 CA.128: 2 residues within 4Å: Ligands: CA.36, CA.82 No protein-ligand interaction detected (PLIP)

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 5 residues within 4Å: Chain A: M.95 Chain C: M.95 Chain E: M.95 Ligands: TRS.58, TRS.104 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain A Water bridges: E:K.98, C:K.98, A:K.98 TRS.35: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.81, TRS.127 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F Water bridges: B:K.98, D:K.98, F:K.98 TRS.58: 5 residues within 4Å: Chain A: M.95 Chain C: M.95 Chain E: M.95 Ligands: TRS.12, TRS.104 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain A Water bridges: C:K.98, E:K.98, A:K.98 TRS.81: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.35, TRS.127 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain F Water bridges: B:K.98, D:K.98, F:K.98 TRS.104: 5 residues within 4Å: Chain A: M.95 Chain C: M.95 Chain E: M.95 Ligands: TRS.12, TRS.58 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain E Water bridges: C:K.98, A:K.98, E:K.98 TRS.127: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.35, TRS.81 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain D Water bridges: F:K.98, B:K.98, D:K.98

21 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)(Covalent)

PG6.14: 6 residues within 4Å: Chain A: Y.305, L.307, D.309, G.310, R.344, A.351 Ligand excluded by PLIP PG6.16: 4 residues within 4Å: Chain A: T.90, K.427, N.428, H.431 Ligand excluded by PLIP PG6.17: 6 residues within 4Å: Chain A: A.7, H.21, A.27, T.28, N.30 Chain B: P.4 Ligand excluded by PLIP PG6.37: 6 residues within 4Å: Chain B: L.307, D.309, G.310, R.344, A.351 Ligands: PG6.38 Ligand excluded by PLIP PG6.38: 4 residues within 4Å: Chain B: Y.305, G.310, R.344 Ligands: PG6.37 Ligand excluded by PLIP PG6.40: 6 residues within 4Å: Chain B: T.90, R.92, K.427, H.431, V.484 Chain F: T.90 Ligand excluded by PLIP PG6.41: 5 residues within 4Å: Chain A: P.4 Chain B: A.7, A.27, V.29, N.30 Ligand excluded by PLIP PG6.60: 6 residues within 4Å: Chain C: Y.305, L.307, D.309, G.310, R.344, A.351 Ligand excluded by PLIP PG6.62: 4 residues within 4Å: Chain C: T.90, K.427, N.428, H.431 Ligand excluded by PLIP PG6.63: 6 residues within 4Å: Chain C: A.7, H.21, A.27, T.28, N.30 Chain D: P.4 Ligand excluded by PLIP PG6.83: 6 residues within 4Å: Chain D: L.307, D.309, G.310, R.344, A.351 Ligands: PG6.84 Ligand excluded by PLIP PG6.84: 4 residues within 4Å: Chain D: Y.305, G.310, R.344 Ligands: PG6.83 Ligand excluded by PLIP PG6.86: 6 residues within 4Å: Chain B: T.90 Chain D: T.90, R.92, K.427, H.431, V.484 Ligand excluded by PLIP PG6.87: 5 residues within 4Å: Chain C: P.4 Chain D: A.7, A.27, V.29, N.30 Ligand excluded by PLIP PG6.106: 6 residues within 4Å: Chain E: Y.305, L.307, D.309, G.310, R.344, A.351 Ligand excluded by PLIP PG6.108: 4 residues within 4Å: Chain E: T.90, K.427, N.428, H.431 Ligand excluded by PLIP PG6.109: 6 residues within 4Å: Chain E: A.7, H.21, A.27, T.28, N.30 Chain F: P.4 Ligand excluded by PLIP PG6.129: 6 residues within 4Å: Chain F: L.307, D.309, G.310, R.344, A.351 Ligands: PG6.130 Ligand excluded by PLIP PG6.130: 4 residues within 4Å: Chain F: Y.305, G.310, R.344 Ligands: PG6.129 Ligand excluded by PLIP PG6.132: 6 residues within 4Å: Chain D: T.90 Chain F: T.90, R.92, K.427, H.431, V.484 Ligand excluded by PLIP PG6.133: 5 residues within 4Å: Chain E: P.4 Chain F: A.7, A.27, V.29, N.30 Ligand excluded by PLIP

36 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.15: 5 residues within 4Å: Chain A: Q.134, F.135, N.137, W.138 Chain E: D.490 Ligand excluded by PLIP PG4.18: 4 residues within 4Å: Chain A: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.19: 3 residues within 4Å: Chain A: R.56, D.58, E.60 Ligand excluded by PLIP PG4.20: 3 residues within 4Å: Chain A: G.50, E.51, R.52 Ligand excluded by PLIP PG4.21: 4 residues within 4Å: Chain A: N.371, G.372, D.377 Ligands: HEC.5 Ligand excluded by PLIP PG4.22: 2 residues within 4Å: Chain A: T.266, L.282 Ligand excluded by PLIP PG4.39: 5 residues within 4Å: Chain B: Q.134, F.135, N.137, W.138 Chain D: R.493 Ligand excluded by PLIP PG4.42: 4 residues within 4Å: Chain B: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.43: 3 residues within 4Å: Chain B: R.56, D.58, E.60 Ligand excluded by PLIP PG4.44: 3 residues within 4Å: Chain B: R.149, T.153, N.218 Ligand excluded by PLIP PG4.45: 5 residues within 4Å: Chain B: L.307, K.332, Q.336, E.466, Y.469 Ligand excluded by PLIP PG4.46: 5 residues within 4Å: Chain B: C.410, H.411, E.413 Chain F: Q.139 Ligands: HEC.28 Ligand excluded by PLIP PG4.61: 5 residues within 4Å: Chain A: D.490 Chain C: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP PG4.64: 4 residues within 4Å: Chain C: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.65: 3 residues within 4Å: Chain C: R.56, D.58, E.60 Ligand excluded by PLIP PG4.66: 3 residues within 4Å: Chain C: G.50, E.51, R.52 Ligand excluded by PLIP PG4.67: 4 residues within 4Å: Chain C: N.371, G.372, D.377 Ligands: HEC.51 Ligand excluded by PLIP PG4.68: 2 residues within 4Å: Chain C: T.266, L.282 Ligand excluded by PLIP PG4.85: 5 residues within 4Å: Chain D: Q.134, F.135, N.137, W.138 Chain F: R.493 Ligand excluded by PLIP PG4.88: 4 residues within 4Å: Chain D: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.89: 3 residues within 4Å: Chain D: R.56, D.58, E.60 Ligand excluded by PLIP PG4.90: 3 residues within 4Å: Chain D: R.149, T.153, N.218 Ligand excluded by PLIP PG4.91: 5 residues within 4Å: Chain D: L.307, K.332, Q.336, E.466, Y.469 Ligand excluded by PLIP PG4.92: 5 residues within 4Å: Chain B: Q.139 Chain D: C.410, H.411, E.413 Ligands: HEC.74 Ligand excluded by PLIP PG4.107: 5 residues within 4Å: Chain C: D.490 Chain E: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP PG4.110: 4 residues within 4Å: Chain E: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.111: 3 residues within 4Å: Chain E: R.56, D.58, E.60 Ligand excluded by PLIP PG4.112: 3 residues within 4Å: Chain E: G.50, E.51, R.52 Ligand excluded by PLIP PG4.113: 4 residues within 4Å: Chain E: N.371, G.372, D.377 Ligands: HEC.97 Ligand excluded by PLIP PG4.114: 2 residues within 4Å: Chain E: T.266, L.282 Ligand excluded by PLIP PG4.131: 5 residues within 4Å: Chain B: R.493 Chain F: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP PG4.134: 4 residues within 4Å: Chain F: R.167, F.168, L.169, S.170 Ligand excluded by PLIP PG4.135: 3 residues within 4Å: Chain F: R.56, D.58, E.60 Ligand excluded by PLIP PG4.136: 3 residues within 4Å: Chain F: R.149, T.153, N.218 Ligand excluded by PLIP PG4.137: 5 residues within 4Å: Chain F: L.307, K.332, Q.336, E.466, Y.469 Ligand excluded by PLIP PG4.138: 5 residues within 4Å: Chain D: Q.139 Chain F: C.410, H.411, E.413 Ligands: HEC.120 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.23: 2 residues within 4Å: Chain A: L.2 Ligands: HEC.30 No protein-ligand interaction detected (PLIP) NA.69: 2 residues within 4Å: Chain C: L.2 Ligands: HEC.76 No protein-ligand interaction detected (PLIP) NA.115: 2 residues within 4Å: Chain E: L.2 Ligands: HEC.122 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimov, A.A. et al., Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase. To be Published

Release Date

2011-10-26

Peptides

Eight-heme nitrite reductase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Eight-heme nitrite reductase

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