SMTL ID : 3f29.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 23 residues within 4Å: Chain A: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.3, SO3.9 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:P.116, A:V.129, A:V.301, A:Y.303, A:Y.303, A:Y.303, A:F.327 Hydrogen bonds: A:A.114, A:A.484, A:N.486 Water bridges: A:H.113, A:H.113, A:H.113, A:R.131, A:H.361 Salt bridges: A:K.90, A:H.113, A:R.131, A:H.361 pi-Stacking: A:H.126, A:H.361 Metal complexes: H2O.1 HEC.2: 18 residues within 4Å: Chain A: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.3, HEC.7 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:H.70, A:Q.73, A:L.225, A:A.290, A:T.396 Hydrogen bonds: A:Q.73, A:T.396, A:T.396 Water bridges: A:K.386, A:K.386 Salt bridges: A:K.386 Metal complexes: A:H.231, A:H.398 HEC.3: 26 residues within 4Å: Chain A: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.1, HEC.2, HEC.4, CA.11 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.116, A:H.383, A:Q.400, A:Q.400 Hydrogen bonds: A:S.84, A:P.116, A:F.121, A:D.125 Water bridges: A:R.81, A:R.81 Metal complexes: A:H.119, A:H.300 HEC.4: 23 residues within 4Å: Chain A: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.3, HEC.5, CA.11 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:H.300, A:E.363, A:E.363, A:F.367, A:H.372, A:V.377, A:P.403, A:I.427, A:N.486, A:F.490, A:F.490 Hydrogen bonds: A:T.402, A:T.402 Water bridges: A:R.81, A:S.84, A:K.431, A:N.486, A:N.486 Salt bridges: A:R.404, A:K.431 Metal complexes: A:H.383, A:H.491 HEC.5: 16 residues within 4Å: Chain A: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, I.427, F.490 Chain C: N.141, W.142, Q.143 Ligands: HEC.4 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C, Hydrophobic interactions: A:V.371, A:V.377, A:P.403, A:W.418, A:I.427, A:F.490, C:W.142, C:Q.143 Metal complexes: A:H.372, A:H.415 Hydrogen bonds: C:W.142 Water bridges: C:Q.143 HEC.6: 23 residues within 4Å: Chain A: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.7, HEC.8 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:A.11, A:F.15, A:I.21, A:I.21, A:V.33, A:T.59, A:I.193, A:L.194, A:F.228, A:P.233, A:P.233, A:F.274 Water bridges: A:R.282 Salt bridges: A:R.239, A:R.276, A:R.282, A:R.282 pi-Stacking: A:H.39 Metal complexes: A:H.39, A:H.234 HEC.7: 17 residues within 4Å: Chain A: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Chain B: H.37, T.68, C.69 Ligands: HEC.2, HEC.6 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A, Water bridges: B:T.68, B:T.68, A:K.29 Hydrophobic interactions: A:K.29, A:K.29, A:T.68, A:H.231 Hydrogen bonds: A:A.236 Salt bridges: A:K.29, A:K.29 Metal complexes: A:H.30, A:H.70 HEC.8: 23 residues within 4Å: Chain A: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.6 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.9, A:A.41, A:V.45, A:A.48, A:M.53, A:P.57 Hydrogen bonds: A:G.277 Water bridges: A:R.56, A:R.276, A:R.276 Salt bridges: A:R.56, A:R.276, A:R.276 Metal complexes: A:H.18, A:H.44 HEC.19: 23 residues within 4Å: Chain B: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.21, SO3.27 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.116, B:V.129, B:V.301, B:Y.303, B:Y.303, B:F.327, B:H.361 Hydrogen bonds: B:A.114, B:A.484, B:N.486 Water bridges: B:H.113, B:A.114, B:R.131, B:H.361 Salt bridges: B:K.90, B:H.113, B:R.131, B:H.361 pi-Stacking: B:Y.303, B:H.361 pi-Cation interactions: B:H.126 Metal complexes: H2O.21 HEC.20: 17 residues within 4Å: Chain B: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.21, HEC.25 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:H.70, B:Q.73, B:Q.73, B:L.225, B:A.290, B:T.396 Hydrogen bonds: B:Q.73, B:T.396 Metal complexes: B:H.231, B:H.398 HEC.21: 26 residues within 4Å: Chain B: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.19, HEC.20, HEC.22, CA.29 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.116, B:H.383, B:Q.400, B:Q.400 Hydrogen bonds: B:S.84, B:R.117, B:F.121 Water bridges: B:R.81, B:R.81, B:R.81, B:Q.400 Metal complexes: B:H.119, B:H.300 HEC.22: 23 residues within 4Å: Chain B: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.21, HEC.23, CA.29 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:H.300, B:E.363, B:E.363, B:F.367, B:H.372, B:V.377, B:P.403, B:I.427, B:N.486, B:F.490, B:F.490 Hydrogen bonds: B:T.402 Water bridges: B:R.81, B:S.84, B:K.431, B:N.486 Salt bridges: B:R.404, B:K.431 Metal complexes: B:H.383, B:H.491 HEC.23: 17 residues within 4Å: Chain B: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Chain F: N.141, W.142, Q.143 Ligands: HEC.22 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain F, Hydrophobic interactions: B:V.377, B:P.403, B:W.418, B:I.427, B:F.490, F:W.142, F:Q.143 Metal complexes: B:H.372, B:H.415 Hydrogen bonds: F:W.142, F:Q.143 Water bridges: F:Q.143 HEC.24: 23 residues within 4Å: Chain B: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.25, HEC.26 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:A.11, B:F.15, B:I.21, B:I.21, B:V.33, B:T.59, B:I.193, B:L.194, B:F.228, B:P.233, B:F.274 Water bridges: B:R.282 Salt bridges: B:R.239, B:R.276, B:R.282, B:R.282 pi-Stacking: B:H.39, B:H.234 Metal complexes: B:H.39, B:H.234 HEC.25: 17 residues within 4Å: Chain A: H.37, T.68, C.69 Chain B: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Ligands: HEC.20, HEC.24 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:K.29, B:K.29, B:V.33, B:T.68, B:H.231, B:A.236 Water bridges: B:K.29 Salt bridges: B:K.29, B:K.29 Metal complexes: B:H.30, B:H.70 HEC.26: 22 residues within 4Å: Chain B: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276 Ligands: HEC.24 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.39, B:A.41, B:V.45, B:M.53, B:P.57 Water bridges: B:H.18, B:R.276, B:R.276 Salt bridges: B:R.56, B:R.276 Metal complexes: B:H.18, B:H.44 HEC.38: 23 residues within 4Å: Chain C: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.40, SO3.46 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:P.116, C:V.129, C:V.301, C:Y.303, C:Y.303, C:Y.303, C:F.327 Hydrogen bonds: C:A.114, C:A.484, C:N.486 Water bridges: C:H.113, C:A.114, C:R.131, C:H.361 Salt bridges: C:K.90, C:H.113, C:R.131, C:H.361 pi-Stacking: C:H.126, C:H.361 Metal complexes: H2O.42 HEC.39: 18 residues within 4Å: Chain C: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.40, HEC.44 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:H.70, C:Q.73, C:L.225, C:A.290, C:T.396 Hydrogen bonds: C:Q.73, C:T.396, C:T.396 Water bridges: C:K.386, C:K.386 Salt bridges: C:K.386 Metal complexes: C:H.231, C:H.398 HEC.40: 26 residues within 4Å: Chain C: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.38, HEC.39, HEC.41, CA.48 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:P.116, C:H.383, C:Q.400, C:Q.400 Hydrogen bonds: C:S.84, C:P.116, C:R.117, C:F.121 Water bridges: C:R.81, C:R.81 Metal complexes: C:H.119, C:H.300 HEC.41: 23 residues within 4Å: Chain C: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.40, HEC.42, CA.48 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:H.300, C:E.363, C:E.363, C:F.367, C:H.372, C:V.377, C:P.403, C:I.427, C:N.486, C:F.490, C:F.490 Hydrogen bonds: C:T.402, C:T.402 Water bridges: C:R.81, C:S.84, C:K.431, C:N.486, C:N.486 Salt bridges: C:R.404, C:K.431 Metal complexes: C:H.383, C:H.491 HEC.42: 16 residues within 4Å: Chain C: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, I.427, F.490 Chain E: N.141, W.142, Q.143 Ligands: HEC.41 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain E, Hydrophobic interactions: C:V.371, C:V.377, C:P.403, C:W.418, C:I.427, C:F.490, E:W.142, E:Q.143 Metal complexes: C:H.372, C:H.415 Hydrogen bonds: E:W.142 Water bridges: E:Q.143 HEC.43: 23 residues within 4Å: Chain C: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.44, HEC.45 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:A.11, C:F.15, C:I.21, C:I.21, C:V.33, C:T.59, C:I.193, C:L.194, C:F.228, C:P.233, C:P.233, C:F.274 Water bridges: C:R.282 Salt bridges: C:R.239, C:R.276, C:R.282, C:R.282 pi-Stacking: C:H.39 Metal complexes: C:H.39, C:H.234 HEC.44: 17 residues within 4Å: Chain C: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Chain D: H.37, T.68, C.69 Ligands: HEC.39, HEC.43 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: C:K.29, C:K.29, C:T.68, C:H.231 Hydrogen bonds: C:A.236 Water bridges: C:K.29 Salt bridges: C:K.29, C:K.29 Metal complexes: C:H.30, C:H.70 HEC.45: 23 residues within 4Å: Chain C: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.43 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:V.9, C:A.41, C:V.45, C:A.48, C:M.53, C:P.57 Hydrogen bonds: C:G.277 Water bridges: C:R.56, C:R.276, C:R.276 Salt bridges: C:R.56, C:R.276, C:R.276 Metal complexes: C:H.18, C:H.44 HEC.56: 23 residues within 4Å: Chain D: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.58, SO3.64 22 PLIP interactions: 21 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:P.116, D:V.129, D:V.301, D:Y.303, D:Y.303, D:F.327, D:H.361 Hydrogen bonds: D:A.114, D:A.484, D:N.486 Water bridges: D:H.113, D:A.114, D:R.131, D:H.361 Salt bridges: D:K.90, D:H.113, D:R.131, D:H.361 pi-Stacking: D:Y.303, D:H.361 pi-Cation interactions: D:H.126 Metal complexes: H2O.63 HEC.57: 17 residues within 4Å: Chain D: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.58, HEC.62 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:H.70, D:Q.73, D:Q.73, D:L.225, D:A.290, D:T.396 Hydrogen bonds: D:Q.73, D:T.396 Metal complexes: D:H.231, D:H.398 HEC.58: 26 residues within 4Å: Chain D: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.56, HEC.57, HEC.59, CA.66 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:P.116, D:H.383, D:Q.400, D:Q.400 Hydrogen bonds: D:S.84, D:R.117, D:F.121, D:D.125 Water bridges: D:R.81, D:R.81, D:R.81, D:Q.400 Metal complexes: D:H.119, D:H.300 HEC.59: 23 residues within 4Å: Chain D: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.58, HEC.60, CA.66 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:H.300, D:E.363, D:E.363, D:F.367, D:H.372, D:V.377, D:P.403, D:I.427, D:N.486, D:F.490, D:F.490 Hydrogen bonds: D:T.402, D:T.402 Water bridges: D:R.81, D:S.84, D:K.431, D:N.486 Salt bridges: D:R.404, D:K.431 Metal complexes: D:H.383, D:H.491 HEC.60: 17 residues within 4Å: Chain B: N.141, W.142, Q.143 Chain D: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Ligands: HEC.59 12 PLIP interactions: 7 interactions with chain D, 5 interactions with chain B, Hydrophobic interactions: D:V.377, D:P.403, D:W.418, D:I.427, D:F.490, B:W.142, B:Q.143 Metal complexes: D:H.372, D:H.415 Hydrogen bonds: B:W.142, B:Q.143 Water bridges: B:Q.143 HEC.61: 23 residues within 4Å: Chain D: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.62, HEC.63 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:A.11, D:F.15, D:I.21, D:I.21, D:V.33, D:T.59, D:I.193, D:L.194, D:F.228, D:P.233, D:F.274 Water bridges: D:R.282 Salt bridges: D:R.239, D:R.276, D:R.282, D:R.282 pi-Stacking: D:H.39, D:H.234 Metal complexes: D:H.39, D:H.234 HEC.62: 17 residues within 4Å: Chain C: H.37, T.68, C.69 Chain D: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Ligands: HEC.57, HEC.61 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:K.29, D:K.29, D:V.33, D:T.68, D:H.231, D:A.236 Water bridges: D:K.29 Salt bridges: D:K.29, D:K.29 Metal complexes: D:H.30, D:H.70 HEC.63: 22 residues within 4Å: Chain D: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276 Ligands: HEC.61 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:H.39, D:A.41, D:V.45, D:M.53, D:P.57 Water bridges: D:H.18, D:R.276, D:R.276 Salt bridges: D:R.56, D:R.276 Metal complexes: D:H.18, D:H.44 HEC.75: 23 residues within 4Å: Chain E: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.77, SO3.83 22 PLIP interactions: 21 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:P.116, E:V.129, E:V.301, E:Y.303, E:Y.303, E:Y.303, E:F.327 Hydrogen bonds: E:A.114, E:A.484, E:N.486 Water bridges: E:H.113, E:H.113, E:H.113, E:R.131, E:H.361 Salt bridges: E:K.90, E:H.113, E:R.131, E:H.361 pi-Stacking: E:H.126, E:H.361 Metal complexes: H2O.84 HEC.76: 18 residues within 4Å: Chain E: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.77, HEC.81 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:H.70, E:Q.73, E:L.225, E:A.290, E:T.396 Hydrogen bonds: E:Q.73, E:T.396, E:T.396 Water bridges: E:K.386, E:K.386 Salt bridges: E:K.386 Metal complexes: E:H.231, E:H.398 HEC.77: 26 residues within 4Å: Chain E: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.75, HEC.76, HEC.78, CA.85 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:P.116, E:H.383, E:Q.400, E:Q.400 Hydrogen bonds: E:S.84, E:P.116, E:R.117, E:F.121 Water bridges: E:R.81, E:R.81 Metal complexes: E:H.119, E:H.300 HEC.78: 23 residues within 4Å: Chain E: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.77, HEC.79, CA.85 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:H.300, E:E.363, E:E.363, E:F.367, E:H.372, E:V.377, E:P.403, E:I.427, E:N.486, E:F.490, E:F.490 Hydrogen bonds: E:T.402 Water bridges: E:R.81, E:S.84, E:K.431, E:N.486, E:N.486 Salt bridges: E:R.404, E:K.431 Metal complexes: E:H.383, E:H.491 HEC.79: 16 residues within 4Å: Chain A: N.141, W.142, Q.143 Chain E: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, I.427, F.490 Ligands: HEC.78 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain A, Hydrophobic interactions: E:V.371, E:V.377, E:P.403, E:W.418, E:I.427, E:F.490, A:W.142, A:Q.143 Metal complexes: E:H.372, E:H.415 Hydrogen bonds: A:W.142 Water bridges: A:Q.143 HEC.80: 23 residues within 4Å: Chain E: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.81, HEC.82 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:A.11, E:F.15, E:I.21, E:I.21, E:V.33, E:T.59, E:I.193, E:L.194, E:F.228, E:P.233, E:P.233, E:F.274 Water bridges: E:R.282 Salt bridges: E:R.239, E:R.276, E:R.282, E:R.282 pi-Stacking: E:H.39 Metal complexes: E:H.39, E:H.234 HEC.81: 17 residues within 4Å: Chain E: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Chain F: H.37, T.68, C.69 Ligands: HEC.76, HEC.80 12 PLIP interactions: 10 interactions with chain E, 2 interactions with chain F, Hydrophobic interactions: E:K.29, E:K.29, E:T.68, E:H.231 Hydrogen bonds: E:A.236 Water bridges: E:K.29, F:T.68, F:T.68 Salt bridges: E:K.29, E:K.29 Metal complexes: E:H.30, E:H.70 HEC.82: 23 residues within 4Å: Chain E: V.9, Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276, G.277 Ligands: HEC.80 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:V.9, E:A.41, E:V.45, E:A.48, E:M.53, E:P.57 Hydrogen bonds: E:G.277 Water bridges: E:R.56, E:R.276, E:R.276 Salt bridges: E:R.56, E:R.276, E:R.276 Metal complexes: E:H.18, E:H.44 HEC.93: 23 residues within 4Å: Chain F: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.179, C.184, C.187, K.188, R.242, C.299, H.300, V.301, Y.303, C.305, F.327, H.361, A.484, N.486 Ligands: HEC.95, SO3.101 23 PLIP interactions: 22 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:P.116, F:V.129, F:V.301, F:Y.303, F:Y.303, F:F.327, F:H.361 Hydrogen bonds: F:A.114, F:A.484, F:N.486 Water bridges: F:H.113, F:H.113, F:H.113, F:R.131, F:H.361 Salt bridges: F:K.90, F:H.113, F:R.131, F:H.361 pi-Stacking: F:Y.303, F:H.361 pi-Cation interactions: F:H.126 Metal complexes: H2O.105 HEC.94: 17 residues within 4Å: Chain F: C.66, H.70, Q.73, F.74, L.225, N.226, C.227, C.230, H.231, A.290, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.95, HEC.99 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:H.70, F:Q.73, F:Q.73, F:L.225, F:A.290, F:T.396 Hydrogen bonds: F:Q.73, F:T.396 Metal complexes: F:H.231, F:H.398 HEC.95: 26 residues within 4Å: Chain F: R.81, S.84, P.116, R.117, S.118, H.119, F.121, M.122, D.125, C.187, K.188, L.225, M.229, M.295, C.296, C.299, H.300, C.379, H.383, M.384, Q.400, R.401 Ligands: HEC.93, HEC.94, HEC.96, CA.103 13 PLIP interactions: 13 interactions with chain F, Hydrophobic interactions: F:P.116, F:H.383, F:Q.400, F:Q.400 Hydrogen bonds: F:S.84, F:F.121, F:D.125 Water bridges: F:R.81, F:R.81, F:R.81, F:Q.400 Metal complexes: F:H.119, F:H.300 HEC.96: 23 residues within 4Å: Chain F: N.293, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.95, HEC.97, CA.103 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:H.300, F:E.363, F:E.363, F:F.367, F:H.372, F:V.377, F:P.403, F:I.427, F:N.486, F:F.490, F:F.490 Hydrogen bonds: F:T.402 Water bridges: F:R.81, F:S.84, F:K.431, F:N.486 Salt bridges: F:R.404, F:K.431 Metal complexes: F:H.383, F:H.491 HEC.97: 17 residues within 4Å: Chain D: N.141, W.142, Q.143 Chain F: V.371, H.372, N.375, V.377, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Ligands: HEC.96 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain D, Hydrophobic interactions: F:V.377, F:P.403, F:W.418, F:I.427, F:F.490, D:W.142, D:Q.143 Metal complexes: F:H.372, F:H.415 Hydrogen bonds: D:W.142, D:Q.143 Water bridges: D:Q.143 HEC.98: 23 residues within 4Å: Chain F: A.11, C.14, F.15, H.18, I.21, H.25, V.33, N.34, C.35, C.38, H.39, T.59, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282 Ligands: HEC.99, HEC.100 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:A.11, F:F.15, F:I.21, F:I.21, F:V.33, F:T.59, F:I.193, F:L.194, F:F.228, F:P.233, F:F.274 Water bridges: F:R.282 Salt bridges: F:R.239, F:R.276, F:R.282, F:R.282 pi-Stacking: F:H.39, F:H.234 Metal complexes: F:H.39, F:H.234 HEC.99: 17 residues within 4Å: Chain E: H.37, T.68, C.69 Chain F: K.29, H.30, V.33, H.37, A.65, C.66, T.68, C.69, H.70, C.227, H.231, A.236 Ligands: HEC.94, HEC.98 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:K.29, F:K.29, F:V.33, F:T.68, F:H.231, F:A.236 Water bridges: F:K.29, E:T.68 Salt bridges: F:K.29, F:K.29 Metal complexes: F:H.30, F:H.70 HEC.100: 22 residues within 4Å: Chain F: Q.13, C.14, C.17, H.18, C.35, H.39, A.41, H.44, V.45, A.48, S.49, S.50, R.51, R.52, M.53, R.56, P.57, T.59, L.194, Q.275, R.276 Ligands: HEC.98 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:H.39, F:A.41, F:V.45, F:M.53, F:P.57 Water bridges: F:H.18, F:R.276, F:R.276 Salt bridges: F:R.56, F:R.276 Metal complexes: F:H.18, F:H.44

9 x SO3: SULFITE ION(Non-covalent)

SO3.9: 6 residues within 4Å: Chain A: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.131, A:Y.303, A:Y.303 SO3.27: 6 residues within 4Å: Chain B: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.131, B:Y.303, B:Y.303 Water bridges: B:R.131 SO3.30: 2 residues within 4Å: Chain B: S.49, S.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.50 Water bridges: B:R.51, B:R.51 SO3.46: 6 residues within 4Å: Chain C: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.131, C:Y.303, C:H.361 Water bridges: C:H.361 SO3.64: 6 residues within 4Å: Chain D: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.56 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.131, D:Y.303, D:H.361 SO3.67: 2 residues within 4Å: Chain D: S.49, S.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.50 Water bridges: D:R.51, D:R.51 SO3.83: 6 residues within 4Å: Chain E: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.75 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.131 Water bridges: E:R.131 SO3.101: 6 residues within 4Å: Chain F: F.109, R.131, Y.303, Q.360, H.361 Ligands: HEC.93 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.131 SO3.104: 2 residues within 4Å: Chain F: S.49, S.50 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.50 Water bridges: F:R.51, F:R.51

12 x CA: CALCIUM ION(Non-covalent)

CA.10: 4 residues within 4Å: Chain A: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.302, A:Y.303, A:K.358, H2O.9, H2O.9 CA.11: 4 residues within 4Å: Chain A: S.84, P.116 Ligands: HEC.3, HEC.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.116, H2O.2, H2O.13, H2O.16 CA.28: 4 residues within 4Å: Chain B: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.302, B:Y.303, B:K.358, H2O.34, H2O.34 CA.29: 4 residues within 4Å: Chain B: S.84, P.116 Ligands: HEC.21, HEC.22 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:P.116, H2O.27, H2O.38, H2O.41 CA.47: 4 residues within 4Å: Chain C: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.302, C:Y.303, C:K.358, H2O.51, H2O.51 CA.48: 4 residues within 4Å: Chain C: S.84, P.116 Ligands: HEC.40, HEC.41 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:P.116, H2O.44, H2O.55, H2O.58 CA.65: 4 residues within 4Å: Chain D: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.302, D:Y.303, D:K.358, H2O.76, H2O.76 CA.66: 4 residues within 4Å: Chain D: S.84, P.116 Ligands: HEC.58, HEC.59 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:P.116, H2O.69, H2O.80, H2O.83 CA.84: 4 residues within 4Å: Chain E: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.302, E:Y.303, E:K.358, H2O.93, H2O.93 CA.85: 4 residues within 4Å: Chain E: S.84, P.116 Ligands: HEC.77, HEC.78 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:P.116, H2O.86, H2O.97, H2O.100 CA.102: 4 residues within 4Å: Chain F: E.302, Y.303, K.358, Q.360 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.302, F:Y.303, F:K.358, H2O.118, H2O.118 CA.103: 4 residues within 4Å: Chain F: S.84, P.116 Ligands: HEC.95, HEC.96 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:P.116, H2O.111, H2O.122, H2O.125

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

PG6.12: 5 residues within 4Å: Chain A: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.348 Water bridges: A:A.355 PG6.31: 5 residues within 4Å: Chain B: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.348 Water bridges: B:A.355 PG6.32: 4 residues within 4Å: Chain B: T.94, K.431, H.435 Chain F: T.94 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.435 PG6.49: 5 residues within 4Å: Chain C: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.348 Water bridges: C:A.355 PG6.68: 5 residues within 4Å: Chain D: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.348 Water bridges: D:A.355 PG6.69: 4 residues within 4Å: Chain B: T.94 Chain D: T.94, K.431, H.435 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.435 PG6.86: 5 residues within 4Å: Chain E: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.348 Water bridges: E:A.355 PG6.105: 5 residues within 4Å: Chain F: L.311, D.313, G.314, R.348, A.355 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.348 Water bridges: F:A.355 PG6.106: 4 residues within 4Å: Chain D: T.94 Chain F: T.94, K.431, H.435 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:H.435

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

PG4.13: 8 residues within 4Å: Chain A: T.94, S.95, D.428, K.431, N.432, H.435, V.488 Chain C: T.94 Ligand excluded by PLIP PG4.14: 4 residues within 4Å: Chain A: Q.138, F.139, N.141, W.142 Ligand excluded by PLIP PG4.15: 4 residues within 4Å: Chain A: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.16: 1 residues within 4Å: Chain A: T.270 Ligand excluded by PLIP PG4.17: 3 residues within 4Å: Chain A: R.60, D.62, E.64 Ligand excluded by PLIP PG4.18: 3 residues within 4Å: Chain A: R.153, T.157, N.222 Ligand excluded by PLIP PG4.33: 4 residues within 4Å: Chain B: Q.138, F.139, W.142 Chain D: D.494 Ligand excluded by PLIP PG4.34: 4 residues within 4Å: Chain B: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PG4.36: 2 residues within 4Å: Chain B: R.60, D.62 Ligand excluded by PLIP PG4.37: 5 residues within 4Å: Chain B: P.307, G.308, Y.309, R.316, V.317 Ligand excluded by PLIP PG4.50: 8 residues within 4Å: Chain C: T.94, S.95, D.428, K.431, N.432, H.435, V.488 Chain E: T.94 Ligand excluded by PLIP PG4.51: 4 residues within 4Å: Chain C: Q.138, F.139, N.141, W.142 Ligand excluded by PLIP PG4.52: 4 residues within 4Å: Chain C: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.53: 1 residues within 4Å: Chain C: T.270 Ligand excluded by PLIP PG4.54: 3 residues within 4Å: Chain C: R.60, D.62, E.64 Ligand excluded by PLIP PG4.55: 3 residues within 4Å: Chain C: R.153, T.157, N.222 Ligand excluded by PLIP PG4.70: 4 residues within 4Å: Chain D: Q.138, F.139, W.142 Chain F: D.494 Ligand excluded by PLIP PG4.71: 4 residues within 4Å: Chain D: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.72: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PG4.73: 2 residues within 4Å: Chain D: R.60, D.62 Ligand excluded by PLIP PG4.74: 5 residues within 4Å: Chain D: P.307, G.308, Y.309, R.316, V.317 Ligand excluded by PLIP PG4.87: 8 residues within 4Å: Chain A: T.94 Chain E: T.94, S.95, D.428, K.431, N.432, H.435, V.488 Ligand excluded by PLIP PG4.88: 4 residues within 4Å: Chain E: Q.138, F.139, N.141, W.142 Ligand excluded by PLIP PG4.89: 4 residues within 4Å: Chain E: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.90: 1 residues within 4Å: Chain E: T.270 Ligand excluded by PLIP PG4.91: 3 residues within 4Å: Chain E: R.60, D.62, E.64 Ligand excluded by PLIP PG4.92: 3 residues within 4Å: Chain E: R.153, T.157, N.222 Ligand excluded by PLIP PG4.107: 4 residues within 4Å: Chain B: D.494 Chain F: Q.138, F.139, W.142 Ligand excluded by PLIP PG4.108: 4 residues within 4Å: Chain F: R.171, F.172, L.173, S.174 Ligand excluded by PLIP PG4.109: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PG4.110: 2 residues within 4Å: Chain F: R.60, D.62 Ligand excluded by PLIP PG4.111: 5 residues within 4Å: Chain F: P.307, G.308, Y.309, R.316, V.317 Ligand excluded by 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

2008-12-09

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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