SMTL ID : 3s7w.1

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.3, NO2.9 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.112, A:V.125, A:V.297, A:Y.299, A:Y.299, A:F.323, A:H.357 Hydrogen bonds: A:A.110, A:A.480, A:N.482 Water bridges: A:H.109, A:A.110, A:R.127, A:H.357 Salt bridges: A:K.86, A:H.109, A:R.127, A:H.357 pi-Stacking: A:H.357 Metal complexes: H2O.19 HEC.2: 17 residues within 4Å: Chain A: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, 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:Q.69, A:L.221, A:A.286, A:T.392 Hydrogen bonds: A:Q.69, A:T.392 Water bridges: A:K.382 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.14 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.112, A:K.184, A:H.379, A:Q.396, A:Q.396 Hydrogen bonds: A:S.80, A:R.113, A:F.117 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: 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, GOL.11, CA.14 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 Water bridges: A:R.77, A:S.80, A:K.427, A:K.427, A:N.482 Salt bridges: A:R.400, A:K.427 Metal complexes: A:H.379, A:H.487 HEC.5: 16 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, I.423, F.486 Chain C: N.137, W.138, Q.139 Ligands: HEC.4 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.373, A:P.399, A:W.414, A:I.423, A:F.486, C:Q.139 Water bridges: A:N.371, 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 19 PLIP interactions: 19 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: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 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:K.25, A:V.29, A:H.227, A:A.232 Hydrogen bonds: A:A.232 Salt bridges: A:K.25, A:K.25 Metal complexes: A:H.26, A:H.66 HEC.8: 22 residues within 4Å: Chain A: Q.9, C.10, C.13, H.14, 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, R.274 Ligands: HEC.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:H.35, A:A.37, A:V.41, A:M.49, A:P.53 Hydrogen bonds: A:R.274 Water bridges: A:R.47, A:R.272, A:R.272, A:G.273 Salt bridges: A:R.52, A:R.272 Metal complexes: A:H.14, A:H.40 HEC.16: 23 residues within 4Å: Chain B: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.18, NO2.24 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.112, B:V.125, B:V.297, B:Y.299, B:Y.299, B:F.323 Hydrogen bonds: B:A.110, B:A.480, B:N.482 Water bridges: B:K.86, B:K.86, B:H.109, B:R.127, B:H.357 Salt bridges: B:K.86, B:H.109, B:R.127, B:H.357 pi-Stacking: B:H.357 Metal complexes: H2O.40 HEC.17: 17 residues within 4Å: Chain B: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.18, HEC.22 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.66, B:Q.69, B:L.221, B:A.286, B:T.392 Hydrogen bonds: B:Q.69, B:T.392, B:T.392 Water bridges: B:K.382 Salt bridges: B:K.382 Metal complexes: B:H.227, B:H.394 HEC.18: 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.16, HEC.17, HEC.19, CA.30 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:P.112, B:H.379 Hydrogen bonds: B:S.80, B:R.113, B:F.117, B:D.121 Water bridges: B:R.77, B:R.77, B:R.77, B:S.114, B:H.122, B:Q.396 Metal complexes: B:H.115, B:H.296 HEC.19: 26 residues within 4Å: Chain B: P.112, 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.18, HEC.20, GOL.26, CA.30 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, B:T.398 Water bridges: B:R.77, B:S.80, B:K.427 Salt bridges: B:R.400, B:K.427 Metal complexes: B:H.379, B:H.487 HEC.20: 16 residues within 4Å: Chain B: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, I.423, F.486 Chain F: N.137, W.138, Q.139 Ligands: HEC.19 13 PLIP interactions: 5 interactions with chain F, 8 interactions with chain B, Hydrophobic interactions: F:W.138, F:Q.139, B:V.367, B:V.373, B:P.399, B:W.414, B:I.423, B:F.486 Hydrogen bonds: F:W.138, F:Q.139 Water bridges: F:Q.139 Metal complexes: B:H.368, B:H.411 HEC.21: 24 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, R.56, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.22, HEC.23 19 PLIP interactions: 19 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: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.22: 16 residues within 4Å: Chain A: H.33, C.65 Chain B: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.17, HEC.21 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:K.25, B:T.64, B:H.227 Salt bridges: B:K.25, B:K.25 Metal complexes: B:H.26, B:H.66 HEC.23: 22 residues within 4Å: Chain B: 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, R.272, G.273 Ligands: HEC.21 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:V.5, B:A.37, B:V.41, B:A.44, B:M.49, B:P.53 Hydrogen bonds: B:G.273 Water bridges: B:R.272, B:R.272, B:R.272 Salt bridges: B:R.52, B:R.272, B:R.272 Metal complexes: B:H.14, B:H.40 HEC.32: 23 residues within 4Å: Chain C: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.34, NO2.40 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:P.112, C:V.125, C:V.297, C:Y.299, C:Y.299, C:F.323, C:H.357 Hydrogen bonds: C:A.110, C:A.480, C:N.482 Water bridges: C:H.109, C:H.109, C:H.109, C:R.127, C:H.357 Salt bridges: C:K.86, C:H.109, C:R.127, C:H.357 pi-Stacking: C:H.357 Metal complexes: H2O.61 HEC.33: 17 residues within 4Å: Chain C: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.34, HEC.38 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:H.66, C:Q.69, C:Q.69, C:L.221, C:A.286, C:T.392 Hydrogen bonds: C:Q.69, C:T.392 Water bridges: C:K.382 Salt bridges: C:K.382 Metal complexes: C:H.227, C:H.394 HEC.34: 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.32, HEC.33, HEC.35, CA.45 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:P.112, C:K.184, C:H.379, C:Q.396, C:Q.396 Hydrogen bonds: C:S.80, C:P.112, C:R.113, C:F.117, C:D.121 Water bridges: C:R.77, C:R.77, C:R.77, C:H.122 Metal complexes: C:H.115, C:H.296 HEC.35: 24 residues within 4Å: Chain C: 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.34, HEC.36, GOL.42, CA.45 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 Water bridges: C:R.77, C:S.80, C:K.427, C:K.427, C:N.482 Salt bridges: C:R.400, C:K.427 Metal complexes: C:H.379, C:H.487 HEC.36: 16 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, I.423, F.486 Chain E: N.137, W.138, Q.139 Ligands: HEC.35 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:V.373, C:P.399, C:W.414, C:I.423, C:F.486, E:Q.139 Water bridges: C:N.371, C:N.371, E:Q.139 Metal complexes: C:H.368, C:H.411 Hydrogen bonds: E:W.138 HEC.37: 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.38, HEC.39 19 PLIP interactions: 19 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: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.38: 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.33, HEC.37 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain C, Water bridges: D:T.64 Hydrophobic interactions: C:K.25, C:V.29, C:H.227, C:A.232 Hydrogen bonds: C:A.232 Salt bridges: C:K.25, C:K.25 Metal complexes: C:H.26, C:H.66 HEC.39: 22 residues within 4Å: Chain C: Q.9, C.10, C.13, H.14, 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, R.274 Ligands: HEC.37 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:H.35, C:A.37, C:V.41, C:M.49, C:P.53 Hydrogen bonds: C:R.274 Water bridges: C:R.47, C:R.272, C:R.272, C:G.273 Salt bridges: C:R.52, C:R.272 Metal complexes: C:H.14, C:H.40 HEC.47: 23 residues within 4Å: Chain D: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.49, NO2.55 20 PLIP interactions: 19 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:P.112, D:V.125, D:V.297, D:Y.299, D:Y.299, D:F.323 Hydrogen bonds: D:A.110, D:A.480, D:N.482 Water bridges: D:K.86, D:K.86, D:H.109, D:R.127, D:H.357 Salt bridges: D:K.86, D:H.109, D:R.127, D:H.357 pi-Stacking: D:H.357 Metal complexes: H2O.82 HEC.48: 17 residues within 4Å: Chain D: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.49, HEC.53 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:H.66, D:Q.69, D:L.221, D:A.286, D:T.392 Hydrogen bonds: D:Q.69, D:T.392, D:T.392 Water bridges: D:K.382 Salt bridges: D:K.382 Metal complexes: D:H.227, D:H.394 HEC.49: 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.47, HEC.48, HEC.50, CA.61 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:P.112, D:H.379 Hydrogen bonds: D:S.80, D:R.113, D:F.117 Water bridges: D:R.77, D:R.77, D:R.77, D:S.114, D:H.122, D:Q.396 Metal complexes: D:H.115, D:H.296 HEC.50: 26 residues within 4Å: Chain D: P.112, 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, GOL.57, CA.61 19 PLIP interactions: 19 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 Water bridges: D:R.77, D:S.80, D:K.427 Salt bridges: D:R.400, D:K.427 Metal complexes: D:H.379, D:H.487 HEC.51: 16 residues within 4Å: Chain B: N.137, W.138, Q.139 Chain D: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, I.423, F.486 Ligands: HEC.50 13 PLIP interactions: 8 interactions with chain D, 5 interactions with chain B, Hydrophobic interactions: D:V.367, D:V.373, D:P.399, D:W.414, D:I.423, D:F.486, B:W.138, B:Q.139 Metal complexes: D:H.368, D:H.411 Hydrogen bonds: B:W.138, B:Q.139 Water bridges: B:Q.139 HEC.52: 24 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, R.56, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.53, HEC.54 19 PLIP interactions: 19 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: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.53: 16 residues within 4Å: Chain C: H.33, C.65 Chain D: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.48, HEC.52 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:K.25, D:T.64, D:H.227 Salt bridges: D:K.25, D:K.25 Metal complexes: D:H.26, D:H.66 HEC.54: 22 residues within 4Å: Chain D: 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, R.272, G.273 Ligands: HEC.52 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:V.5, D:A.37, D:V.41, D:A.44, D:M.49, D:P.53 Hydrogen bonds: D:G.273 Water bridges: D:R.272, D:R.272, D:R.272 Salt bridges: D:R.52, D:R.272, D:R.272 Metal complexes: D:H.14, D:H.40 HEC.63: 23 residues within 4Å: Chain E: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.65, NO2.71 20 PLIP interactions: 19 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:P.112, E:V.125, E:V.297, E:Y.299, E:Y.299, E:F.323, E:H.357 Hydrogen bonds: E:A.110, E:A.480, E:N.482 Water bridges: E:H.109, E:A.110, E:R.127, E:H.357 Salt bridges: E:K.86, E:H.109, E:R.127, E:H.357 pi-Stacking: E:H.357 Metal complexes: H2O.102 HEC.64: 17 residues within 4Å: Chain E: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.65, HEC.69 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:H.66, E:Q.69, E:Q.69, E:L.221, E:A.286, E:T.392 Hydrogen bonds: E:Q.69, E:T.392 Water bridges: E:K.382 Salt bridges: E:K.382 Metal complexes: E:H.227, E:H.394 HEC.65: 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.63, HEC.64, HEC.66, CA.76 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:P.112, E:K.184, E:H.379, E:Q.396, E:Q.396 Hydrogen bonds: E:S.80, E:R.113, E:F.117, E:D.121 Water bridges: E:R.77, E:R.77, E:R.77, E:H.122 Metal complexes: E:H.115, E:H.296 HEC.66: 24 residues within 4Å: Chain E: 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.65, HEC.67, GOL.73, CA.76 22 PLIP interactions: 22 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, E:T.398 Water bridges: E:R.77, E:S.80, E:K.427, E:K.427, E:N.482 Salt bridges: E:R.400, E:K.427 Metal complexes: E:H.379, E:H.487 HEC.67: 16 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, I.423, F.486 Ligands: HEC.66 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.373, E:P.399, E:W.414, E:I.423, E:F.486, A:Q.139 Water bridges: E:N.371, E:N.371, A:Q.139 Metal complexes: E:H.368, E:H.411 Hydrogen bonds: A:W.138 HEC.68: 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.69, HEC.70 19 PLIP interactions: 19 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: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.69: 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.64, HEC.68 9 PLIP interactions: 9 interactions with chain E, Hydrophobic interactions: E:K.25, E:V.29, E:H.227, E:A.232 Hydrogen bonds: E:A.232 Salt bridges: E:K.25, E:K.25 Metal complexes: E:H.26, E:H.66 HEC.70: 22 residues within 4Å: Chain E: Q.9, C.10, C.13, H.14, 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, R.274 Ligands: HEC.68 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:H.35, E:A.37, E:V.41, E:M.49, E:P.53 Hydrogen bonds: E:R.274 Water bridges: E:R.47, E:R.272, E:R.272, E:G.273 Salt bridges: E:R.52, E:R.272 Metal complexes: E:H.14, E:H.40 HEC.78: 23 residues within 4Å: Chain F: H.109, A.110, P.112, D.121, H.122, V.125, R.127, 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.80, NO2.86 19 PLIP interactions: 18 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:P.112, F:V.125, F:V.297, F:Y.299, F:Y.299, F:F.323 Hydrogen bonds: F:A.110, F:A.480, F:N.482 Water bridges: F:K.86, F:K.86, F:R.127, F:H.357 Salt bridges: F:K.86, F:H.109, F:R.127, F:H.357 pi-Stacking: F:H.357 Metal complexes: H2O.124 HEC.79: 17 residues within 4Å: Chain F: C.62, H.66, Q.69, F.70, L.221, N.222, C.223, C.226, H.227, A.286, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.80, HEC.84 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:H.66, F:Q.69, F:L.221, F:A.286, F:T.392 Hydrogen bonds: F:Q.69, F:T.392, F:T.392 Water bridges: F:K.382 Salt bridges: F:K.382 Metal complexes: F:H.227, F:H.394 HEC.80: 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.78, HEC.79, HEC.81, CA.92 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:P.112, F:H.379 Hydrogen bonds: F:S.80, F:F.117 Water bridges: F:R.77, F:R.77, F:R.77, F:S.114, F:H.122, F:Q.396 Metal complexes: F:H.115, F:H.296 HEC.81: 26 residues within 4Å: Chain F: P.112, 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.80, HEC.82, GOL.88, CA.92 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, F:T.398 Water bridges: F:R.77, F:S.80, F:K.427 Salt bridges: F:R.400, F:K.427 Metal complexes: F:H.379, F:H.487 HEC.82: 16 residues within 4Å: Chain D: N.137, W.138, Q.139 Chain F: V.367, H.368, N.371, V.373, P.399, A.406, C.407, C.410, H.411, W.414, I.423, F.486 Ligands: HEC.81 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain F, Hydrophobic interactions: D:W.138, D:Q.139, F:V.367, F:V.373, F:P.399, F:W.414, F:I.423, F:F.486 Hydrogen bonds: D:W.138, D:Q.139 Water bridges: D:Q.139 Metal complexes: F:H.368, F:H.411 HEC.83: 24 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, R.56, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.84, HEC.85 19 PLIP interactions: 19 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: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.84: 16 residues within 4Å: Chain E: H.33, C.65 Chain F: K.25, H.26, V.29, H.33, A.61, C.62, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.79, HEC.83 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:K.25, F:T.64, F:H.227 Salt bridges: F:K.25, F:K.25 Metal complexes: F:H.26, F:H.66 HEC.85: 22 residues within 4Å: Chain F: 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, R.272, G.273 Ligands: HEC.83 15 PLIP interactions: 15 interactions with chain F, Hydrophobic interactions: F:V.5, F:A.37, F:V.41, F:A.44, F:M.49, F:P.53 Hydrogen bonds: F:G.273 Water bridges: F:R.272, F:R.272, F:R.272 Salt bridges: F:R.52, F:R.272, F:R.272 Metal complexes: F:H.14, F:H.40

6 x NO2: NITRITE ION(Non-covalent)

NO2.9: 6 residues within 4Å: Chain A: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:Y.299 NO2.24: 6 residues within 4Å: Chain B: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.16 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.127, B:K.184, B:H.357 Water bridges: B:R.127, B:Y.299, B:Q.356, B:Q.356 NO2.40: 6 residues within 4Å: Chain C: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.32 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.127, C:K.184 Water bridges: C:Y.299, C:Y.299 NO2.55: 6 residues within 4Å: Chain D: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.47 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.127, D:Y.299 Water bridges: D:Y.299, D:Y.299, D:Q.356, D:Q.356 NO2.71: 6 residues within 4Å: Chain E: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.63 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.127, E:Y.299 NO2.86: 6 residues within 4Å: Chain F: F.105, R.127, K.184, Y.299, H.357 Ligands: HEC.78 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.127, F:Y.299, F:H.357 Water bridges: F:Q.356, F:Q.356

12 x CA: CALCIUM ION(Non-covalent)

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.12, H2O.12 CA.14: 4 residues within 4Å: Chain A: P.112 Ligands: HEC.3, HEC.4, GOL.11 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.112, H2O.15 CA.25: 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.33, H2O.33 CA.30: 4 residues within 4Å: Chain B: P.112 Ligands: HEC.18, HEC.19, GOL.26 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.112, H2O.25, H2O.36 CA.41: 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.53, H2O.53 CA.45: 4 residues within 4Å: Chain C: P.112 Ligands: HEC.34, HEC.35, GOL.42 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:P.112, H2O.56 CA.56: 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.75, H2O.75 CA.61: 4 residues within 4Å: Chain D: P.112 Ligands: HEC.49, HEC.50, GOL.57 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:P.112, H2O.67, H2O.78 CA.72: 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.95, H2O.95 CA.76: 4 residues within 4Å: Chain E: P.112 Ligands: HEC.65, HEC.66, GOL.73 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:P.112, H2O.98 CA.87: 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.117, H2O.117 CA.92: 4 residues within 4Å: Chain F: P.112 Ligands: HEC.80, HEC.81, GOL.88 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:P.112, H2O.109, H2O.120

21 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: R.92, E.111, P.112, N.482 Ligands: HEC.4, CA.14 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain A: K.436, W.440, I.500, K.504 Chain C: D.97, A.106, F.107, Q.171 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: Q.134, F.135, N.137, W.138 Chain E: R.493 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain B: R.92, E.111, P.112, N.482 Ligands: HEC.19, CA.30 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain B: W.440, I.500, K.504 Chain F: D.97, A.106, F.107, Q.171 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain B: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: D.164, Q.165, S.208, E.209, V.210 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain C: R.92, E.111, P.112, N.482 Ligands: HEC.35, CA.45 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain C: K.436, W.440, I.500, K.504 Chain E: D.97, A.106, F.107, Q.171 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain A: R.493 Chain C: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP GOL.57: 6 residues within 4Å: Chain D: R.92, E.111, P.112, N.482 Ligands: HEC.50, CA.61 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain B: D.97, A.106, F.107, Q.171 Chain D: W.440, I.500, K.504 Ligand excluded by PLIP GOL.59: 4 residues within 4Å: Chain D: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain D: D.164, Q.165, S.208, E.209, V.210 Ligand excluded by PLIP GOL.73: 6 residues within 4Å: Chain E: R.92, E.111, P.112, N.482 Ligands: HEC.66, CA.76 Ligand excluded by PLIP GOL.74: 8 residues within 4Å: Chain A: D.97, A.106, F.107, Q.171 Chain E: K.436, W.440, I.500, K.504 Ligand excluded by PLIP GOL.75: 5 residues within 4Å: Chain C: R.493 Chain E: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP GOL.88: 6 residues within 4Å: Chain F: R.92, E.111, P.112, N.482 Ligands: HEC.81, CA.92 Ligand excluded by PLIP GOL.89: 7 residues within 4Å: Chain D: D.97, A.106, F.107, Q.171 Chain F: W.440, I.500, K.504 Ligand excluded by PLIP GOL.90: 4 residues within 4Å: Chain F: Q.134, F.135, N.137, W.138 Ligand excluded by PLIP GOL.91: 5 residues within 4Å: Chain F: D.164, Q.165, S.208, E.209, V.210 Ligand excluded by PLIP

6 x AZI: AZIDE ION(Non-covalent)

AZI.15: 6 residues within 4Å: Chain A: S.72, E.75, V.383, Y.391, S.393, S.395 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.75, A:Y.391, A:Y.391 Water bridges: A:E.75, A:S.393, A:S.393, A:S.395, A:S.395 AZI.31: 3 residues within 4Å: Chain B: R.52, V.54, T.55 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.55 Water bridges: B:T.55, B:T.55, B:T.55 AZI.46: 6 residues within 4Å: Chain C: S.72, E.75, V.383, Y.391, S.393, S.395 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.75, C:Y.391 Water bridges: C:E.75, C:S.393, C:S.393, C:S.395, C:S.395 AZI.62: 3 residues within 4Å: Chain D: R.52, V.54, T.55 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.55 Water bridges: D:R.52, D:T.55, D:T.55 AZI.77: 6 residues within 4Å: Chain E: S.72, E.75, V.383, Y.391, S.393, S.395 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.75, E:Y.391, E:S.393 Water bridges: E:E.75, E:S.393, E:S.393, E:S.395, E:S.395 AZI.93: 3 residues within 4Å: Chain F: R.52, V.54, T.55 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.55, F:T.55 Water bridges: F:R.52, F:P.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimov, A.A. et al., Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine. To be Published

Release Date

2011-07-27

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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