SMTL ID : 4q5c.1

TvNiR in complex with sulfite, middle dose data set

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 24 residues within 4Å: Chain A: 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.3, SO3.9 21 PLIP interactions: 21 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:N.482 Water bridges: A:H.109, A:H.109, A:H.109, A:R.127, A:H.357, A:H.357 Salt bridges: A:K.86, A:H.109, A:R.127, A:H.357 pi-Stacking: A:H.357 HEC.2: 19 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, ACT.16 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, A:T.392 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 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:P.112, A:L.221, A:H.379 Hydrogen bonds: A:S.80, A:P.112, A:R.113, 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 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:H.296, A:E.359, A:E.359, A:F.363, 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: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: 19 residues within 4Å: Chain A: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, A.422, I.423, F.486 Chain C: N.137, W.138, Q.139 Ligands: HEC.4 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.367, A:V.373, A:P.399, A:W.414, A:W.414, A:A.422, A:I.423, A:F.486, C:Q.139 Metal complexes: A:H.368, A:H.411 Hydrogen bonds: C:W.138, C:Q.139 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 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.7, A:F.11, 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, C.65 Ligands: HEC.2, HEC.6, ACT.16 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:K.25, A:K.25, A:T.64, A:H.227 Salt bridges: A:K.25, A:K.25 Metal complexes: A:H.26, A:H.66 HEC.8: 21 residues within 4Å: Chain A: 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 Ligands: HEC.6 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:A.37, A:V.41, A:M.49, A:P.53 Hydrogen bonds: A:R.274 Water bridges: A:H.14, 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.17: 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.19, SO3.26 17 PLIP interactions: 17 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:N.482 Water bridges: B:R.127, B:H.357, B:H.357 Salt bridges: B:K.86, B:H.109, B:R.127, B:H.357 HEC.18: 19 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.19, HEC.23, ACT.25 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.66, B:Q.69, B:Q.69, B:L.221, B:A.286, B:T.392 Hydrogen bonds: B:Q.69, B:T.392 Water bridges: B:K.382 Salt bridges: B:K.382 Metal complexes: B:H.227, B:H.394 HEC.19: 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.17, HEC.18, HEC.20 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:P.112, B:L.221, B:H.379 Hydrogen bonds: B:S.80, B:R.113 Water bridges: B:R.77, B:R.77, B:Q.396 Metal complexes: B:H.115, B:H.296 HEC.20: 23 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.19, HEC.21 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:H.296, B:E.359, B:E.359, B:F.363, B:V.373, B:P.399, B:I.423, B:N.482, B:F.486, B:F.486 Water bridges: 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.21: 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, A.422, I.423, F.486, P.489 Chain F: N.137, W.138, Q.139 Ligands: HEC.20 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain F, Hydrophobic interactions: B:V.367, B:V.373, B:P.399, B:W.414, B:W.414, B:A.422, B:I.423, B:F.486, F:Q.139 Water bridges: B:N.371 Metal complexes: B:H.368, B:H.411 Hydrogen bonds: F:W.138, F:Q.139 HEC.22: 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.23, HEC.24 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.23: 18 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, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.18, HEC.22, ACT.25 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:K.25, B:V.29 Water bridges: B:K.389 Salt bridges: B:K.25, B:K.25 Metal complexes: B:H.26, B:H.66 HEC.24: 23 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.22, SO3.29 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:V.41, B:M.49, B:P.53 Water bridges: B:R.52, B:R.52, B:R.272 Salt bridges: B:R.52, B:R.272 Metal complexes: B:H.14, B:H.40 HEC.32: 24 residues within 4Å: Chain C: 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.34, SO3.40 20 PLIP interactions: 20 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:N.482 Water bridges: C:H.109, C:A.110, C:R.127, C:H.357, C:H.357 Salt bridges: C:K.86, C:H.109, C:R.127, C:H.357 pi-Stacking: C:H.357 HEC.33: 19 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.34, HEC.38, ACT.47 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, C:T.392 Salt bridges: C:K.382 Metal complexes: C:H.227, C:H.394 HEC.34: 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.32, HEC.33, HEC.35 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:P.112, C:L.221, C:H.379 Hydrogen bonds: C:S.80, C:P.112, C:R.113 Water bridges: C:R.77, C:R.77 Metal complexes: C:H.115, C:H.296 HEC.35: 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.34, HEC.36 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:H.296, C:E.359, C:E.359, C:F.363, 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: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.36: 19 residues within 4Å: Chain C: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, A.422, I.423, F.486 Chain E: N.137, W.138, Q.139 Ligands: HEC.35 13 PLIP interactions: 3 interactions with chain E, 10 interactions with chain C, Hydrophobic interactions: E:Q.139, C:V.367, C:V.373, C:P.399, C:W.414, C:W.414, C:A.422, C:I.423, C:F.486 Hydrogen bonds: E:W.138, E:Q.139 Metal complexes: C:H.368, C:H.411 HEC.37: 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.38, HEC.39 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:A.7, C:F.11, 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.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, C.65 Ligands: HEC.33, HEC.37, ACT.47 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:K.25, C:K.25, C:T.64, C:H.227 Salt bridges: C:K.25, C:K.25 Metal complexes: C:H.26, C:H.66 HEC.39: 21 residues within 4Å: Chain C: 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 Ligands: HEC.37 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.37, C:V.41, C:M.49, C:P.53 Hydrogen bonds: C:R.274 Water bridges: C:H.14, 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.48: 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.50, SO3.57 17 PLIP interactions: 17 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:N.482 Water bridges: D:R.127, D:H.357, D:H.357 Salt bridges: D:K.86, D:H.109, D:R.127, D:H.357 HEC.49: 19 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.50, HEC.54, ACT.56 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:H.66, D:Q.69, D:Q.69, D:L.221, D:A.286, D:T.392 Hydrogen bonds: D:Q.69, D:T.392 Water bridges: D:K.382 Salt bridges: D:K.382 Metal complexes: D:H.227, D:H.394 HEC.50: 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.48, HEC.49, HEC.51 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:P.112, D:L.221, D:H.379 Hydrogen bonds: D:S.80, D:R.113, D:D.121 Water bridges: D:R.77, D:R.77, D:Q.396 Metal complexes: D:H.115, D:H.296 HEC.51: 23 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.50, HEC.52 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:H.296, D:E.359, D:E.359, D:F.363, 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: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.52: 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, A.422, I.423, F.486, P.489 Ligands: HEC.51 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain D, Hydrophobic interactions: B:Q.139, D:V.367, D:V.373, D:P.399, D:W.414, D:W.414, D:A.422, D:I.423, D:F.486 Hydrogen bonds: B:W.138, B:Q.139 Water bridges: D:N.371 Metal complexes: D:H.368, D:H.411 HEC.53: 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.54, HEC.55 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.54: 18 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, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.49, HEC.53, ACT.56 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:K.25, D:V.29 Water bridges: D:K.389 Salt bridges: D:K.25, D:K.25 Metal complexes: D:H.26, D:H.66 HEC.55: 23 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.53, SO3.60 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:V.41, D:M.49, D:P.53 Water bridges: D:R.52, D:R.52, D:R.272 Salt bridges: D:R.52, D:R.272 Metal complexes: D:H.14, D:H.40 HEC.63: 24 residues within 4Å: Chain E: 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.65, SO3.71 21 PLIP interactions: 21 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:N.482 Water bridges: E:H.109, E:H.109, E:H.109, E:R.127, E:H.357, E:H.357 Salt bridges: E:K.86, E:H.109, E:R.127, E:H.357 pi-Stacking: E:H.357 HEC.64: 19 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.65, HEC.69, ACT.78 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, E:T.392 Salt bridges: E:K.382 Metal complexes: E:H.227, E:H.394 HEC.65: 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.63, HEC.64, HEC.66 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:P.112, E:L.221, E:H.379 Hydrogen bonds: E:S.80, E:P.112, E:R.113 Water bridges: E:R.77, E:R.77 Metal complexes: E:H.115, E:H.296 HEC.66: 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.65, HEC.67 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:H.296, E:E.359, E:E.359, E:F.363, E:V.373, E:P.399, E:I.423, E:N.482, E:F.486, E:F.486 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.67: 19 residues within 4Å: Chain A: N.137, W.138, Q.139 Chain E: V.367, H.368, N.371, V.373, C.378, P.399, A.406, C.407, C.410, H.411, W.414, A.419, A.422, I.423, F.486 Ligands: HEC.66 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.367, E:V.373, E:P.399, E:W.414, E:W.414, E:A.422, E:I.423, E:F.486, A:Q.139 Metal complexes: E:H.368, E:H.411 Hydrogen bonds: A:W.138, A:Q.139 HEC.68: 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.69, HEC.70 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:A.7, E:F.11, 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.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, C.65 Ligands: HEC.64, HEC.68, ACT.78 8 PLIP interactions: 8 interactions with chain E, Hydrophobic interactions: E:K.25, E:K.25, E:T.64, E:H.227 Salt bridges: E:K.25, E:K.25 Metal complexes: E:H.26, E:H.66 HEC.70: 21 residues within 4Å: Chain E: 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 Ligands: HEC.68 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:A.37, E:V.41, E:M.49, E:P.53 Hydrogen bonds: E:R.274 Water bridges: E:H.14, 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.79: 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.81, SO3.88 18 PLIP interactions: 18 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:N.482 Water bridges: F:H.109, F:R.127, F:H.357, F:H.357 Salt bridges: F:K.86, F:H.109, F:R.127, F:H.357 HEC.80: 19 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, S.288, M.291, M.380, Y.391, T.392, H.394 Ligands: HEC.81, HEC.85, ACT.87 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:H.66, F:Q.69, F:Q.69, F:L.221, F:A.286, F:T.392 Hydrogen bonds: F:Q.69, F:T.392 Water bridges: F:K.382 Salt bridges: F:K.382 Metal complexes: F:H.227, F:H.394 HEC.81: 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.79, HEC.80, HEC.82 11 PLIP interactions: 11 interactions with chain F, Hydrophobic interactions: F:P.112, F:L.221, F:H.379 Hydrogen bonds: F:S.80, F:R.113, F:D.121 Water bridges: F:R.77, F:R.77, F:Q.396 Metal complexes: F:H.115, F:H.296 HEC.82: 23 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.81, HEC.83 17 PLIP interactions: 17 interactions with chain F, Hydrophobic interactions: F:H.296, F:E.359, F:E.359, F:F.363, F:V.373, F:P.399, F:I.423, F:N.482, F:F.486, F:F.486 Water bridges: 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.83: 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, A.422, I.423, F.486, P.489 Ligands: HEC.82 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain D, Hydrophobic interactions: F:V.367, F:V.373, F:P.399, F:W.414, F:W.414, F:A.422, F:I.423, F:F.486, D:Q.139 Water bridges: F:N.371 Metal complexes: F:H.368, F:H.411 Hydrogen bonds: D:W.138, D:Q.139 HEC.84: 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.85, HEC.86 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.85: 18 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, T.64, C.65, H.66, C.223, H.227, A.232 Ligands: HEC.80, HEC.84, ACT.87 7 PLIP interactions: 7 interactions with chain F, Hydrophobic interactions: F:K.25, F:V.29 Water bridges: F:K.389 Salt bridges: F:K.25, F:K.25 Metal complexes: F:H.26, F:H.66 HEC.86: 23 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.84, SO3.91 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:V.41, F:M.49, F:P.53 Water bridges: F:R.52, F:R.52, F:R.272 Salt bridges: F:R.52, F:R.272 Metal complexes: F:H.14, F:H.40

15 x SO3: SULFITE ION(Non-covalent)

SO3.9: 6 residues within 4Å: Chain A: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.127 Water bridges: A:Y.299, A:Q.356 SO3.12: 5 residues within 4Å: Chain A: H.14, T.15, Q.16, I.17, F.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.14, A:Q.16, A:Q.16, A:I.17 Water bridges: A:H.14 SO3.15: 2 residues within 4Å: Chain A: S.46, R.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.46, A:R.47, A:R.47 SO3.26: 6 residues within 4Å: Chain B: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.127, B:Y.299 Water bridges: B:R.127 SO3.29: 6 residues within 4Å: Chain B: H.14, T.15, Q.16, I.17, F.270 Ligands: HEC.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.14, B:Q.16, B:Q.16, B:I.17 SO3.40: 6 residues within 4Å: Chain C: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.32 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.127, C:Y.299 Water bridges: C:Q.356, C:Q.356 SO3.43: 5 residues within 4Å: Chain C: H.14, T.15, Q.16, I.17, F.270 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.14, C:Q.16, C:Q.16, C:I.17 Water bridges: C:H.14 SO3.46: 2 residues within 4Å: Chain C: S.46, R.47 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.46, C:R.47, C:R.47 SO3.57: 6 residues within 4Å: Chain D: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.48 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.127, D:Y.299, D:Y.299, D:H.357 Water bridges: D:Q.356, D:Q.356 SO3.60: 6 residues within 4Å: Chain D: H.14, T.15, Q.16, I.17, F.270 Ligands: HEC.55 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.14, D:Q.16, D:Q.16, D:I.17 SO3.71: 6 residues within 4Å: Chain E: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.63 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.127, E:H.357 Water bridges: E:Y.299, E:Y.299 SO3.74: 5 residues within 4Å: Chain E: H.14, T.15, Q.16, I.17, F.270 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.14, E:Q.16, E:Q.16, E:I.17 Water bridges: E:H.14 SO3.77: 2 residues within 4Å: Chain E: S.46, R.47 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.46, E:R.47, E:R.47 SO3.88: 6 residues within 4Å: Chain F: F.105, R.127, Y.299, Q.356, H.357 Ligands: HEC.79 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.127, F:Y.299, F:Y.299 Water bridges: F:Y.299, F:Y.299 SO3.91: 6 residues within 4Å: Chain F: H.14, T.15, Q.16, I.17, F.270 Ligands: HEC.86 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.14, F:Q.16, F:Q.16, F:I.17

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.2, H2O.5 CA.27: 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.26, H2O.28 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.48, H2O.50 CA.58: 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.71, H2O.73 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.93, H2O.95 CA.89: 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.116, H2O.118

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.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 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.135, A:W.138, A:W.138, A:W.138, A:V.141, E:Y.425, E:Y.429 Hydrogen bonds: A:R.83, A:R.83, A:F.135 MPD.28: 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 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.135, 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 MPD.42: 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 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:Y.425, A:Y.429, C:F.135, C:W.138, C:W.138, C:W.138, C:V.141 Hydrogen bonds: C:R.83, C:R.83, C:F.135 MPD.59: 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 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.135, 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 MPD.73: 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 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:F.135, E:W.138, E:W.138, E:W.138, E:V.141, C:Y.425, C:Y.429 Hydrogen bonds: E:R.83, E:R.83, E:F.135 MPD.90: 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 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.135, 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

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.13: 4 residues within 4Å: Chain A: Y.194, K.267, T.269, D.276 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.194, A:T.269 Water bridges: A:K.267, A:D.276, A:D.276 Salt bridges: A:K.267 ACT.16: 5 residues within 4Å: Chain A: H.66, K.389 Chain B: T.64 Ligands: HEC.2, HEC.7 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.69, A:Q.69, A:K.389, A:K.389 Salt bridges: A:H.66 ACT.25: 5 residues within 4Å: Chain A: T.64 Chain B: H.66, K.389 Ligands: HEC.18, HEC.23 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:T.67, B:Q.69, B:K.389 Salt bridges: B:H.66 ACT.30: 5 residues within 4Å: Chain B: Y.194, K.267, T.269, D.276, A.279 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.194, B:T.269, B:A.279 Water bridges: B:K.267 Salt bridges: B:K.267 ACT.44: 4 residues within 4Å: Chain C: Y.194, K.267, T.269, D.276 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.194, C:T.269 Water bridges: C:K.267 Salt bridges: C:K.267 ACT.47: 5 residues within 4Å: Chain C: H.66, K.389 Chain D: T.64 Ligands: HEC.33, HEC.38 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Water bridges: C:Q.69, C:K.389, C:K.389, D:T.67 Salt bridges: C:H.66 ACT.56: 5 residues within 4Å: Chain C: T.64 Chain D: H.66, K.389 Ligands: HEC.49, HEC.54 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Water bridges: D:Q.69, D:K.389, C:T.67 Salt bridges: D:H.66 ACT.61: 5 residues within 4Å: Chain D: Y.194, K.267, T.269, D.276, A.279 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:Y.194, D:T.269, D:A.279 Water bridges: D:D.197, D:K.267 Salt bridges: D:K.267 ACT.75: 4 residues within 4Å: Chain E: Y.194, K.267, T.269, D.276 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.194, E:T.269 Water bridges: E:K.267, E:D.276, E:D.276 Salt bridges: E:K.267 ACT.78: 5 residues within 4Å: Chain E: H.66, K.389 Chain F: T.64 Ligands: HEC.64, HEC.69 5 PLIP interactions: 5 interactions with chain E Water bridges: E:Q.69, E:Q.69, E:K.389, E:K.389 Salt bridges: E:H.66 ACT.87: 5 residues within 4Å: Chain E: T.64 Chain F: H.66, K.389 Ligands: HEC.80, HEC.85 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Water bridges: F:Q.69, F:Q.69, F:K.389, E:T.67 Salt bridges: F:H.66 ACT.92: 5 residues within 4Å: Chain F: Y.194, K.267, T.269, D.276, A.279 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Y.194, F:T.269, F:A.279 Water bridges: F:K.267 Salt bridges: F:K.267

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

TRS.14: 8 residues within 4Å: Chain A: M.95, K.98 Chain C: M.95, K.98 Chain E: M.95, K.98 Ligands: TRS.45, TRS.76 13 PLIP interactions: 6 interactions with chain C, 3 interactions with chain E, 4 interactions with chain A Water bridges: C:K.98, C:K.98, C:K.98, C:K.98, C:K.98, C:D.446, E:K.98, E:K.98, A:K.98, A:K.98, A:K.98, A:K.98 Hydrogen bonds: E:K.98 TRS.31: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.62, TRS.93 No protein-ligand interaction detected (PLIP) TRS.45: 8 residues within 4Å: Chain A: M.95, K.98 Chain C: M.95, K.98 Chain E: M.95, K.98 Ligands: TRS.14, TRS.76 13 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 6 interactions with chain E Water bridges: C:K.98, C:K.98, C:K.98, C:K.98, A:K.98, A:K.98, E:K.98, E:K.98, E:K.98, E:K.98, E:K.98, E:D.446 Hydrogen bonds: A:K.98 TRS.62: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.31, TRS.93 No protein-ligand interaction detected (PLIP) TRS.76: 8 residues within 4Å: Chain A: M.95, K.98 Chain C: M.95, K.98 Chain E: M.95, K.98 Ligands: TRS.14, TRS.45 13 PLIP interactions: 4 interactions with chain E, 3 interactions with chain C, 6 interactions with chain A Water bridges: E:K.98, E:K.98, E:K.98, E:K.98, C:K.98, C:K.98, A:K.98, A:K.98, A:K.98, A:K.98, A:K.98, A:D.446 Hydrogen bonds: C:K.98 TRS.93: 5 residues within 4Å: Chain B: M.95 Chain D: M.95 Chain F: M.95 Ligands: TRS.31, TRS.62 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazarenko, V.A. et al., X-ray-induced changes in the active site structure of octaheme cytochrome c nitrite reductase and its substrate complexes. To be Published

Release Date

2014-09-03

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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