SMTL ID : 3rkh.1

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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 19 PLIP interactions: 19 interactions with chain A, 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:R.127, A:H.357 Salt bridges: A:K.86, A:H.109, A:R.127, A:H.357 pi-Stacking: A:H.122 HEC.2: 18 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.3, HEC.7 13 PLIP interactions: 13 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, A:T.392 Water bridges: A:K.382 Salt bridges: A:K.382 Metal complexes: A:H.227, A:H.394 HEC.3: 25 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 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.112, A:M.118, A:L.221, A:H.379, A:Q.396 Hydrogen bonds: A:S.80, A:P.112, A:R.113, A:F.117, A:D.121 Water bridges: A:R.77, A:R.77 Metal complexes: A:H.115, A:H.296 HEC.4: 23 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 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:H.296, A:E.359, A:E.359, A:F.363, 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:R.92, A:T.398, A:T.398 Water bridges: 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, I.426, F.486, P.489 Chain C: W.138, Q.139 Ligands: HEC.4 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:V.367, A:V.373, A:P.399, A:W.414, A:I.423, A:I.426, A:F.486, C:W.138, C:Q.139 Water bridges: A:H.368, A:N.371, A:H.487 Metal complexes: A:H.368, A:H.411 HEC.6: 24 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, R.56, 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, C.65, H.66, C.223, H.227, A.232 Chain B: H.33, T.64, C.65 Ligands: HEC.2, HEC.6, HEC.18 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:K.25, A:K.25, A:V.29, A:A.232, B:T.64 Hydrogen bonds: A:A.232 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 15 PLIP interactions: 15 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 pi-Stacking: A:H.14, A:H.14 Metal complexes: A:H.14, A:H.40 HEC.12: 26 residues within 4Å: Chain B: H.109, A.110, E.111, 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.14, NO2.20 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:P.112, B:V.125, B:A.128, B:V.297, B:Y.299, B:Y.299, B:Y.299, B:F.323 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-Cation interactions: B:H.122 HEC.13: 20 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, S.288, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.14, HEC.18 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:H.66, B:Q.69, B:Q.69, B:F.73, B:L.221, B:A.286, B:M.291, B:T.392 Hydrogen bonds: B:Q.69, B:T.392 Water bridges: B:K.382, B:K.382 Salt bridges: B:K.382 Metal complexes: B:H.227, B:H.394 HEC.14: 25 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.12, HEC.13, HEC.15 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.112, B:L.221, B:H.379, B:Q.396 Hydrogen bonds: B:S.80, B:R.113, B:F.117 Water bridges: B:R.77, B:R.77, B:Q.396 Metal complexes: B:H.115, B:H.296 HEC.15: 24 residues within 4Å: Chain B: R.92, 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.14, HEC.16 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:H.296, B:E.359, B:E.359, B:F.363, 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:R.92, B:T.398 Water bridges: B:S.80, B:K.427, B:N.482, B:N.482 Salt bridges: B:R.400, B:K.427 Metal complexes: B:H.379, B:H.487 HEC.16: 20 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, I.426, F.486, P.489 Chain F: N.137, W.138, Q.139 Ligands: HEC.15 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain F, Hydrophobic interactions: B:V.367, B:V.373, B:P.399, B:W.414, B:I.423, B:I.426, B:F.486, F:W.138, F:Q.139 Water bridges: B:V.367 Metal complexes: B:H.368, B:H.411 Hydrogen bonds: F:W.138, F:Q.139 HEC.17: 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.18, HEC.19 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.18: 17 residues within 4Å: Chain A: H.33, T.64, 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: HEC.7, HEC.13, HEC.17 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:K.25, B:K.25, B:V.29, B:A.232, A:T.64 Salt bridges: B:K.25, B:K.25 Metal complexes: B:H.26, B:H.66 HEC.19: 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.17 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.37, B:V.41, B:M.49, B:P.53 Water bridges: B:R.272, B:R.272 Salt bridges: B:R.52, B:R.272 Metal complexes: B:H.14, B:H.40 HEC.23: 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.25, NO2.31 18 PLIP interactions: 18 interactions with chain C, 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:R.127, C:H.357 Salt bridges: C:K.86, C:H.109, C:R.127, C:H.357 pi-Stacking: C:H.122 HEC.24: 18 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.25, HEC.29 13 PLIP interactions: 13 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, C:T.392 Water bridges: C:K.382 Salt bridges: C:K.382 Metal complexes: C:H.227, C:H.394 HEC.25: 25 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.23, HEC.24, HEC.26 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:P.112, C:M.118, C:L.221, 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 Metal complexes: C:H.115, C:H.296 HEC.26: 23 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.25, HEC.27 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:H.296, C:E.359, C:E.359, C:F.363, 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:R.92, C:T.398, C:T.398 Water bridges: 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.27: 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, I.426, F.486, P.489 Chain E: W.138, Q.139 Ligands: HEC.26 14 PLIP interactions: 2 interactions with chain E, 12 interactions with chain C, Hydrophobic interactions: E:W.138, E:Q.139, C:V.367, C:V.373, C:P.399, C:W.414, C:I.423, C:I.426, C:F.486 Water bridges: C:H.368, C:N.371, C:H.487 Metal complexes: C:H.368, C:H.411 HEC.28: 24 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, R.56, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.29, HEC.30 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.29: 17 residues within 4Å: Chain C: K.25, H.26, V.29, H.33, A.61, C.62, C.65, H.66, C.223, H.227, A.232 Chain D: H.33, T.64, C.65 Ligands: HEC.24, HEC.28, HEC.40 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:K.25, C:K.25, C:V.29, C:A.232, D:T.64 Hydrogen bonds: C:A.232 Salt bridges: C:K.25, C:K.25 Metal complexes: C:H.26, C:H.66 HEC.30: 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.28 15 PLIP interactions: 15 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 pi-Stacking: C:H.14, C:H.14 Metal complexes: C:H.14, C:H.40 HEC.34: 26 residues within 4Å: Chain D: H.109, A.110, E.111, 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.36, NO2.42 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:P.112, D:V.125, D:A.128, D:V.297, D:Y.299, D:Y.299, D:Y.299, D:F.323 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-Cation interactions: D:H.122 HEC.35: 20 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, S.288, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.36, HEC.40 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:H.66, D:Q.69, D:Q.69, D:F.73, D:L.221, D:A.286, D:M.291, D:T.392 Hydrogen bonds: D:Q.69, D:T.392 Water bridges: D:K.382, D:K.382 Salt bridges: D:K.382 Metal complexes: D:H.227, D:H.394 HEC.36: 25 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.34, HEC.35, HEC.37 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:P.112, D:L.221, D:H.379, 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:Q.396 Metal complexes: D:H.115, D:H.296 HEC.37: 24 residues within 4Å: Chain D: R.92, 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.36, HEC.38 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:H.296, D:E.359, D:E.359, D:F.363, 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:R.92, D:T.398, D:T.398 Water bridges: D:S.80, D:K.427, D:N.482, D:N.482 Salt bridges: D:R.400, D:K.427 Metal complexes: D:H.379, D:H.487 HEC.38: 20 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, I.426, F.486, P.489 Ligands: HEC.37 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain D, Hydrophobic interactions: B:W.138, B:Q.139, D:V.367, D:V.373, D:P.399, D:W.414, D:I.423, D:I.426, D:F.486 Hydrogen bonds: B:W.138, B:Q.139 Water bridges: D:V.367 Metal complexes: D:H.368, D:H.411 HEC.39: 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.40, HEC.41 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.40: 17 residues within 4Å: Chain C: H.33, T.64, 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: HEC.29, HEC.35, HEC.39 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:K.25, D:K.25, D:V.29, D:A.232, C:T.64 Salt bridges: D:K.25, D:K.25 Metal complexes: D:H.26, D:H.66 HEC.41: 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.39 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:A.37, D:V.41, D:M.49, D:P.53 Water bridges: D:R.272, D:R.272 Salt bridges: D:R.52, D:R.272 Metal complexes: D:H.14, D:H.40 HEC.45: 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.47, NO2.53 19 PLIP interactions: 19 interactions with chain E, 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:R.127, E:H.357 Salt bridges: E:K.86, E:H.109, E:R.127, E:H.357 pi-Stacking: E:H.122 HEC.46: 18 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.47, HEC.51 13 PLIP interactions: 13 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, E:T.392 Water bridges: E:K.382 Salt bridges: E:K.382 Metal complexes: E:H.227, E:H.394 HEC.47: 25 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.45, HEC.46, HEC.48 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:P.112, E:M.118, E:L.221, 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 Metal complexes: E:H.115, E:H.296 HEC.48: 23 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.47, HEC.49 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:H.296, E:E.359, E:E.359, E:F.363, 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:R.92, E:T.398 Water bridges: 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.49: 18 residues within 4Å: Chain A: 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, I.426, F.486, P.489 Ligands: HEC.48 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain A, Hydrophobic interactions: E:V.367, E:V.373, E:P.399, E:W.414, E:I.423, E:I.426, E:F.486, A:W.138, A:Q.139 Water bridges: E:H.368, E:N.371, E:H.487 Metal complexes: E:H.368, E:H.411 HEC.50: 24 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, R.56, I.189, L.190, F.224, P.229, H.230, R.235, F.270, R.272, R.278 Ligands: HEC.51, HEC.52 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.51: 17 residues within 4Å: Chain E: K.25, H.26, V.29, H.33, A.61, C.62, C.65, H.66, C.223, H.227, A.232 Chain F: H.33, T.64, C.65 Ligands: HEC.46, HEC.50, HEC.62 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:K.25, E:K.25, E:V.29, E:A.232, F:T.64 Hydrogen bonds: E:A.232 Salt bridges: E:K.25, E:K.25 Metal complexes: E:H.26, E:H.66 HEC.52: 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.50 15 PLIP interactions: 15 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 pi-Stacking: E:H.14, E:H.14 Metal complexes: E:H.14, E:H.40 HEC.56: 26 residues within 4Å: Chain F: H.109, A.110, E.111, 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.58, NO2.64 19 PLIP interactions: 19 interactions with chain F, Hydrophobic interactions: F:P.112, F:V.125, F:A.128, F:V.297, F:Y.299, F:Y.299, F:Y.299, F:F.323 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-Cation interactions: F:H.122 HEC.57: 20 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, S.288, M.291, M.380, K.382, Y.391, T.392, H.394 Ligands: HEC.58, HEC.62 15 PLIP interactions: 15 interactions with chain F, Hydrophobic interactions: F:H.66, F:Q.69, F:Q.69, F:F.73, F:L.221, F:A.286, F:M.291, F:T.392 Hydrogen bonds: F:Q.69, F:T.392 Water bridges: F:K.382, F:K.382 Salt bridges: F:K.382 Metal complexes: F:H.227, F:H.394 HEC.58: 25 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.56, HEC.57, HEC.59 13 PLIP interactions: 13 interactions with chain F, Hydrophobic interactions: F:P.112, F:L.221, F:H.379, 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:Q.396 Metal complexes: F:H.115, F:H.296 HEC.59: 24 residues within 4Å: Chain F: R.92, 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.58, HEC.60 22 PLIP interactions: 22 interactions with chain F, Hydrophobic interactions: F:H.296, F:E.359, F:E.359, F:F.363, 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:R.92, F:T.398 Water bridges: F:S.80, F:K.427, F:N.482, F:N.482 Salt bridges: F:R.400, F:K.427 Metal complexes: F:H.379, F:H.487 HEC.60: 20 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, I.426, F.486, P.489 Ligands: HEC.59 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain D, Hydrophobic interactions: F:V.367, F:V.373, F:P.399, F:W.414, F:I.423, F:I.426, F:F.486, D:W.138, D:Q.139 Water bridges: F:V.367 Metal complexes: F:H.368, F:H.411 Hydrogen bonds: D:W.138, D:Q.139 HEC.61: 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.62, HEC.63 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.62: 17 residues within 4Å: Chain E: H.33, T.64, 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: HEC.51, HEC.57, HEC.61 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:K.25, F:K.25, F:V.29, F:A.232, E:T.64 Salt bridges: F:K.25, F:K.25 Metal complexes: F:H.26, F:H.66 HEC.63: 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.61 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:A.37, F:V.41, F:M.49, F:P.53 Water bridges: F:R.272, F:R.272 Salt bridges: F:R.52, F:R.272 Metal complexes: F:H.14, F:H.40

6 x NO2: NITRITE ION(Non-covalent)

NO2.9: 7 residues within 4Å: Chain A: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:H.357 NO2.20: 7 residues within 4Å: Chain B: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.127, B:K.184, B:Y.299, B:H.357 NO2.31: 7 residues within 4Å: Chain C: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.127, C:K.184, C:Y.299, C:H.357 NO2.42: 7 residues within 4Å: Chain D: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.127, D:H.357 NO2.53: 7 residues within 4Å: Chain E: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.45 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.127, E:K.184, E:H.357 NO2.64: 7 residues within 4Å: Chain F: F.105, R.127, K.184, Y.299, Q.356, H.357 Ligands: HEC.56 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.127, F:K.184, F:H.357

6 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.17, H2O.17 CA.21: 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.43, H2O.43 CA.32: 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.68, H2O.68 CA.43: 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.94, H2O.94 CA.54: 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.119, H2O.119 CA.65: 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.145, H2O.145

6 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.11: 9 residues within 4Å: Chain A: R.83, V.124, Q.134, F.135, W.138, V.141 Chain E: Y.425, Y.429, R.493 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain A Hydrophobic interactions: E:Y.425, A:V.124, A:F.135, A:W.138, A:W.138, A:V.141 Water bridges: E:R.493 Hydrogen bonds: A:R.83, A:R.83, A:F.135, A:F.135 MRD.22: 9 residues within 4Å: Chain B: R.83, V.124, Q.134, F.135, W.138, V.141 Chain D: Y.425, Y.429, R.493 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.135, B:W.138, B:W.138, B:W.138, B:V.141, D:Y.425, D:Y.429 Hydrogen bonds: B:R.83, B:R.83, B:F.135 MRD.33: 9 residues within 4Å: Chain A: Y.425, Y.429, R.493 Chain C: R.83, V.124, Q.134, F.135, W.138, V.141 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:Y.425, C:V.124, C:F.135, C:W.138, C:W.138, C:V.141 Water bridges: A:R.493 Hydrogen bonds: C:R.83, C:R.83, C:F.135, C:F.135 MRD.44: 9 residues within 4Å: Chain D: R.83, V.124, Q.134, F.135, W.138, V.141 Chain F: Y.425, Y.429, R.493 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.135, D:W.138, D:W.138, D:W.138, D:V.141, F:Y.425, F:Y.429 Hydrogen bonds: D:R.83, D:R.83, D:F.135 MRD.55: 9 residues within 4Å: Chain C: Y.425, Y.429, R.493 Chain E: R.83, V.124, Q.134, F.135, W.138, V.141 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:V.124, E:F.135, E:W.138, E:W.138, E:V.141, C:Y.425 Hydrogen bonds: E:R.83, E:R.83, E:F.135, E:F.135 Water bridges: C:R.493 MRD.66: 9 residues within 4Å: Chain B: Y.425, Y.429, R.493 Chain F: R.83, V.124, Q.134, F.135, W.138, V.141 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.135, F:W.138, F:W.138, F:W.138, F:V.141, B:Y.425, B:Y.429 Hydrogen bonds: F:R.83, F:R.83, F:F.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimov, A.A. et al., Covalent modifications of the catalytic tyrosine in octahaem cytochrome c nitrite reductase and their effect on the enzyme activity. Acta Crystallogr.,Sect.D (2012)

Release Date

2011-06-15

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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