SMTL ID : 2ot4.1

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 8 residues within 4Å: Chain A: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.13, H2O.13 CA.13: 8 residues within 4Å: Chain B: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.29, H2O.29 CA.27: 8 residues within 4Å: Chain C: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.60, H2O.60 CA.39: 8 residues within 4Å: Chain D: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.53: 8 residues within 4Å: Chain E: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.107, H2O.107 CA.65: 8 residues within 4Å: Chain F: E.302, Y.303, N.304, F.328, Y.335, K.358, L.359, 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.123, H2O.123

48 x HEC: HEME C(Covalent)

HEC.2: 31 residues within 4Å: Chain A: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, A.484, N.486 Ligands: HEC.4, HEC.5 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:V.129, A:A.132, A:V.301, A:Y.303, A:Y.303, A:F.327 Hydrogen bonds: A:A.114, A:A.484, A:N.486 Water bridges: A:K.90, A:K.90, A:H.113, A:H.113, A:R.131 Salt bridges: A:K.90, A:H.113, A:H.113, A:R.131, A:H.361 pi-Stacking: A:Y.303, A:H.361 Metal complexes: H2O.9 HEC.3: 23 residues within 4Å: Chain A: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, Y.395, T.396, H.398 Ligands: HEC.4, HEC.8 10 PLIP interactions: 10 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 Water bridges: A:T.396 Metal complexes: A:H.231, A:H.398 HEC.4: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.2, HEC.3, HEC.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.116, A:L.225, A:H.383, A:Q.400 Hydrogen bonds: A:S.84, A:P.116, A:R.117, A:F.121, A:D.125 Water bridges: A:R.81, A:R.81, A:H.126 Metal complexes: A:H.119, A:H.300 HEC.5: 27 residues within 4Å: Chain A: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.2, HEC.4, HEC.6 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:H.300, A:E.363, A:E.363, A:F.367, A:V.377, A:P.403, A:I.427, A:N.486, A:F.490, A:F.490 Hydrogen bonds: A:R.96, A:T.402, A:T.402 Water bridges: A:S.84, A:R.404, A:R.404, A:K.431, A:N.486 Salt bridges: A:R.404, A:K.431 Metal complexes: A:H.383, A:H.491 HEC.6: 24 residues within 4Å: Chain A: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, N.413, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Chain C: N.141, W.142, Q.143 Ligands: HEC.5 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C, Hydrophobic interactions: A:V.371, A:V.377, A:P.403, A:W.418, A:I.427, A:I.430, A:F.490, C:W.142, C:Q.143 Water bridges: A:D.494, C:Q.143 Metal complexes: A:H.372, A:H.415 Hydrogen bonds: C:W.142, C:Q.143 HEC.7: 29 residues within 4Å: Chain A: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.8, HEC.9, MRD.10 18 PLIP interactions: 18 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:F.274 Water bridges: A:H.234 Salt bridges: A:R.239, A:R.276, A:R.282, A:R.282 Metal complexes: A:H.39, A:H.234 HEC.8: 22 residues within 4Å: Chain A: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain B: H.37, T.68, C.69 Ligands: HEC.3, HEC.7, HEC.20 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:K.29, A:K.29, A:V.33, A:T.68 Hydrogen bonds: A:A.236 Water bridges: A:K.29, B:T.68 Salt bridges: A:K.29, A:K.29 Metal complexes: A:H.30, A:H.70 HEC.9: 26 residues within 4Å: Chain A: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.7, MRD.11 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.9, A:A.41, A:V.45, 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 pi-Stacking: A:H.18, A:H.44 Metal complexes: A:H.18, A:H.44 HEC.14: 30 residues within 4Å: Chain B: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, N.186, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, N.486 Ligands: HEC.16 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:V.129, B:A.132, B:V.301, B:Y.303, B:Y.303, B:F.327 Hydrogen bonds: B:A.114, B:A.484, B:N.486 Water bridges: B:K.90, B:K.90, B:H.113, B:R.131 Salt bridges: B:K.90, B:H.113, B:H.113, B:R.131, B:H.361 pi-Stacking: B:Y.303, B:H.361 Metal complexes: H2O.40 HEC.15: 25 residues within 4Å: Chain B: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, K.386, Y.395, T.396, H.398, Q.400 Ligands: HEC.16, HEC.20 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.70, B:Q.73, B:F.77, B:L.225, B:A.290, B:T.396 Hydrogen bonds: B:Q.73, B:T.396 Water bridges: B:K.386 Salt bridges: B:K.386 Metal complexes: B:H.231, B:H.398 HEC.16: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.14, HEC.15, HEC.17 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.116, B:K.188, B:H.383 Hydrogen bonds: B:S.84, B:R.117, B:F.121 Water bridges: B:R.81, B:R.81, B:H.126, B:Q.400 Metal complexes: B:H.119, B:H.300 HEC.17: 26 residues within 4Å: Chain B: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.16, HEC.18 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:H.300, B:E.363, B:E.363, B:F.367, B:V.377, B:P.403, B:I.427, B:N.486, B:F.490, B:F.490 Hydrogen bonds: B:R.96, B:T.402, B:T.402 Water bridges: B:S.84, B:R.96, B:R.404, B:R.404, B:K.431, B:N.486 Salt bridges: B:R.404, B:K.431 Metal complexes: B:H.383, B:H.491 HEC.18: 23 residues within 4Å: Chain B: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Chain F: N.141, W.142, Q.143 Ligands: HEC.17 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain F, Hydrophobic interactions: B:V.371, B:V.377, B:P.403, B:W.418, B:I.427, B:I.430, B:F.490, F:W.142, F:Q.143 Water bridges: B:D.494, F:Q.143 Metal complexes: B:H.372, B:H.415 Hydrogen bonds: F:W.142, F:Q.143 HEC.19: 29 residues within 4Å: Chain B: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.20, HEC.21, MRD.23 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:A.11, B:F.15, 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:H.234 Salt bridges: B:R.239, B:R.276, B:R.282, B:R.282 Metal complexes: B:H.39, B:H.234 HEC.20: 22 residues within 4Å: Chain A: H.37, T.68, C.69 Chain B: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.8, HEC.15, HEC.19 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:K.29, B:K.29, B:T.68, B:H.231 Water bridges: B:K.29, A:T.68 Salt bridges: B:K.29, B:K.29 Metal complexes: B:H.30, B:H.70 HEC.21: 25 residues within 4Å: Chain B: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.19 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:A.41, B:V.45, B:M.53, B:P.57 Water bridges: B:H.18, B:Q.275, B:R.276, B:R.276, B:R.278, B:R.278 Salt bridges: B:R.56, B:R.276 pi-Stacking: B:H.18 Metal complexes: B:H.18, B:H.44 HEC.28: 31 residues within 4Å: Chain C: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, A.484, N.486 Ligands: HEC.30, HEC.31 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:V.129, C:A.132, C:V.301, C:Y.303, C:Y.303, C:F.327 Hydrogen bonds: C:A.114, C:A.484, C:N.486 Water bridges: C:K.90, C:K.90, C:H.113, C:H.113, C:R.131 Salt bridges: C:K.90, C:H.113, C:H.113, C:R.131, C:H.361 pi-Stacking: C:Y.303, C:H.361 Metal complexes: H2O.56 HEC.29: 23 residues within 4Å: Chain C: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, Y.395, T.396, H.398 Ligands: HEC.30, HEC.34 10 PLIP interactions: 10 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 Water bridges: C:T.396 Metal complexes: C:H.231, C:H.398 HEC.30: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.28, HEC.29, HEC.31 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:P.116, C:L.225, C:H.383, 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, C:H.126 Metal complexes: C:H.119, C:H.300 HEC.31: 27 residues within 4Å: Chain C: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.28, HEC.30, HEC.32 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:H.300, C:E.363, C:E.363, C:F.367, C:V.377, C:P.403, C:I.427, C:N.486, C:F.490, C:F.490 Hydrogen bonds: C:R.96, C:T.402, C:T.402 Water bridges: C:S.84, C:R.404, C:R.404, C:K.431, C:N.486 Salt bridges: C:R.404, C:K.431 Metal complexes: C:H.383, C:H.491 HEC.32: 24 residues within 4Å: Chain C: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, N.413, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Chain E: N.141, W.142, Q.143 Ligands: HEC.31 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain E, Hydrophobic interactions: C:V.371, C:V.377, C:P.403, C:W.418, C:I.427, C:I.430, C:F.490, E:W.142, E:Q.143 Water bridges: C:D.494, E:Q.143 Metal complexes: C:H.372, C:H.415 Hydrogen bonds: E:W.142, E:Q.143 HEC.33: 29 residues within 4Å: Chain C: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.34, HEC.35, MRD.36 18 PLIP interactions: 18 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:F.274 Water bridges: C:H.234 Salt bridges: C:R.239, C:R.276, C:R.282, C:R.282 Metal complexes: C:H.39, C:H.234 HEC.34: 22 residues within 4Å: Chain C: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain D: H.37, T.68, C.69 Ligands: HEC.29, HEC.33, HEC.46 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:K.29, C:K.29, C:V.33, C:T.68 Hydrogen bonds: C:A.236 Water bridges: C:K.29, D:T.68 Salt bridges: C:K.29, C:K.29 Metal complexes: C:H.30, C:H.70 HEC.35: 26 residues within 4Å: Chain C: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.33, MRD.37 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:V.9, C:A.41, C:V.45, 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 pi-Stacking: C:H.18, C:H.44 Metal complexes: C:H.18, C:H.44 HEC.40: 30 residues within 4Å: Chain D: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, N.186, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, N.486 Ligands: HEC.42 21 PLIP interactions: 20 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:V.129, D:A.132, D:V.301, D:Y.303, D:Y.303, D:F.327 Hydrogen bonds: D:A.114, D:A.484, D:N.486 Water bridges: D:K.90, D:K.90, D:H.113, D:R.131 Salt bridges: D:K.90, D:H.113, D:H.113, D:R.131, D:H.361 pi-Stacking: D:Y.303, D:H.361 Metal complexes: H2O.87 HEC.41: 25 residues within 4Å: Chain D: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, K.386, Y.395, T.396, H.398, Q.400 Ligands: HEC.42, HEC.46 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:H.70, D:Q.73, D:F.77, D:L.225, D:A.290, D:T.396 Hydrogen bonds: D:Q.73, D:T.396 Water bridges: D:K.386 Salt bridges: D:K.386 Metal complexes: D:H.231, D:H.398 HEC.42: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.40, HEC.41, HEC.43 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:P.116, D:K.188, D:H.383 Hydrogen bonds: D:S.84, D:R.117, D:F.121, D:D.125 Water bridges: D:R.81, D:R.81, D:H.126, D:Q.400 Metal complexes: D:H.119, D:H.300 HEC.43: 26 residues within 4Å: Chain D: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.42, HEC.44 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:H.300, D:E.363, D:E.363, D:F.367, D:V.377, D:P.403, D:I.427, D:N.486, D:F.490, D:F.490 Hydrogen bonds: D:R.96, D:T.402, D:T.402 Water bridges: D:S.84, D:R.96, D:R.404, D:R.404, D:K.431, D:N.486 Salt bridges: D:R.404, D:K.431 Metal complexes: D:H.383, D:H.491 HEC.44: 23 residues within 4Å: Chain B: N.141, W.142, Q.143 Chain D: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Ligands: HEC.43 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain B, Hydrophobic interactions: D:V.371, D:V.377, D:P.403, D:W.418, D:I.427, D:I.430, D:F.490, B:W.142, B:Q.143 Water bridges: D:D.494, B:Q.143 Metal complexes: D:H.372, D:H.415 Hydrogen bonds: B:W.142, B:Q.143 HEC.45: 29 residues within 4Å: Chain D: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.46, HEC.47, MRD.49 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:A.11, D:F.15, 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:H.234 Salt bridges: D:R.239, D:R.276, D:R.282, D:R.282 Metal complexes: D:H.39, D:H.234 HEC.46: 22 residues within 4Å: Chain C: H.37, T.68, C.69 Chain D: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.34, HEC.41, HEC.45 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:K.29, D:K.29, D:T.68, D:H.231 Water bridges: D:K.29, C:T.68 Salt bridges: D:K.29, D:K.29 Metal complexes: D:H.30, D:H.70 HEC.47: 25 residues within 4Å: Chain D: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.45 15 PLIP interactions: 15 interactions with chain D, Hydrophobic interactions: D:A.41, D:V.45, D:M.53, D:P.57 Water bridges: D:H.18, D:Q.275, D:R.276, D:R.276, D:R.278, D:R.278 Salt bridges: D:R.56, D:R.276 pi-Stacking: D:H.18 Metal complexes: D:H.18, D:H.44 HEC.54: 31 residues within 4Å: Chain E: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, A.484, N.486 Ligands: HEC.56, HEC.57 22 PLIP interactions: 21 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:V.129, E:A.132, E:V.301, E:Y.303, E:Y.303, E:F.327 Hydrogen bonds: E:A.114, E:A.484, E:N.486 Water bridges: E:K.90, E:K.90, E:H.113, E:H.113, E:R.131 Salt bridges: E:K.90, E:H.113, E:H.113, E:R.131, E:H.361 pi-Stacking: E:Y.303, E:H.361 Metal complexes: H2O.103 HEC.55: 23 residues within 4Å: Chain E: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, Y.395, T.396, H.398 Ligands: HEC.56, HEC.60 10 PLIP interactions: 10 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 Water bridges: E:T.396 Metal complexes: E:H.231, E:H.398 HEC.56: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.54, HEC.55, HEC.57 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:P.116, E:L.225, E:H.383, 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, E:H.126 Metal complexes: E:H.119, E:H.300 HEC.57: 27 residues within 4Å: Chain E: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.54, HEC.56, HEC.58 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:H.300, E:E.363, E:E.363, E:F.367, E:V.377, E:P.403, E:I.427, E:N.486, E:F.490, E:F.490 Hydrogen bonds: E:R.96, E:T.402, E:T.402 Water bridges: E:S.84, E:R.404, E:R.404, E:K.431, E:N.486 Salt bridges: E:R.404, E:K.431 Metal complexes: E:H.383, E:H.491 HEC.58: 24 residues within 4Å: Chain A: N.141, W.142, Q.143 Chain E: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, N.413, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Ligands: HEC.57 15 PLIP interactions: 10 interactions with chain E, 5 interactions with chain A, Hydrophobic interactions: E:V.371, E:V.377, E:P.403, E:W.418, E:I.427, E:I.430, E:F.490, A:W.142, A:Q.143 Water bridges: E:D.494, A:Q.143 Metal complexes: E:H.372, E:H.415 Hydrogen bonds: A:W.142, A:Q.143 HEC.59: 29 residues within 4Å: Chain E: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.60, HEC.61, MRD.62 18 PLIP interactions: 18 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:F.274 Water bridges: E:H.234 Salt bridges: E:R.239, E:R.276, E:R.282, E:R.282 Metal complexes: E:H.39, E:H.234 HEC.60: 22 residues within 4Å: Chain E: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Chain F: H.37, T.68, C.69 Ligands: HEC.55, HEC.59, HEC.72 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:K.29, E:K.29, E:V.33, E:T.68 Hydrogen bonds: E:A.236 Water bridges: E:K.29, F:T.68 Salt bridges: E:K.29, E:K.29 Metal complexes: E:H.30, E:H.70 HEC.61: 26 residues within 4Å: Chain E: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.59, MRD.63 16 PLIP interactions: 16 interactions with chain E, Hydrophobic interactions: E:V.9, E:A.41, E:V.45, 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 pi-Stacking: E:H.18, E:H.44 Metal complexes: E:H.18, E:H.44 HEC.66: 30 residues within 4Å: Chain F: H.113, A.114, E.115, P.116, D.125, H.126, V.129, R.131, A.132, A.179, A.180, N.181, V.183, C.184, N.186, C.187, K.188, R.242, Q.298, C.299, H.300, V.301, Y.303, C.305, N.306, F.327, H.361, E.363, N.486 Ligands: HEC.68 21 PLIP interactions: 20 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:V.129, F:A.132, F:V.301, F:Y.303, F:Y.303, F:F.327 Hydrogen bonds: F:A.114, F:A.484, F:N.486 Water bridges: F:K.90, F:K.90, F:H.113, F:R.131 Salt bridges: F:K.90, F:H.113, F:H.113, F:R.131, F:H.361 pi-Stacking: F:Y.303, F:H.361 Metal complexes: H2O.134 HEC.67: 25 residues within 4Å: Chain F: L.63, C.66, H.70, Q.73, F.74, F.77, L.225, N.226, C.227, M.229, C.230, H.231, A.290, S.292, M.295, C.296, A.380, M.384, K.386, Y.395, T.396, H.398, Q.400 Ligands: HEC.68, HEC.72 12 PLIP interactions: 12 interactions with chain F, Hydrophobic interactions: F:H.70, F:Q.73, F:F.77, F:L.225, F:A.290, F:T.396 Hydrogen bonds: F:Q.73, F:T.396 Water bridges: F:K.386 Salt bridges: F:K.386 Metal complexes: F:H.231, F:H.398 HEC.68: 29 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, S.292, M.295, C.296, Q.298, C.299, H.300, C.379, A.380, H.383, M.384, Q.400, R.401, T.402 Ligands: HEC.66, HEC.67, HEC.69 13 PLIP interactions: 13 interactions with chain F, Hydrophobic interactions: F:P.116, F:K.188, F:H.383 Hydrogen bonds: F:S.84, F:R.117, F:F.121, F:D.125 Water bridges: F:R.81, F:R.81, F:H.126, F:Q.400 Metal complexes: F:H.119, F:H.300 HEC.69: 26 residues within 4Å: Chain F: R.96, P.116, N.293, C.296, H.300, E.363, A.364, F.367, H.372, V.377, A.378, C.379, D.381, C.382, H.383, T.402, P.403, R.404, I.427, K.431, N.486, S.487, F.490, H.491 Ligands: HEC.68, HEC.70 23 PLIP interactions: 23 interactions with chain F, Hydrophobic interactions: F:H.300, F:E.363, F:E.363, F:F.367, F:V.377, F:P.403, F:I.427, F:N.486, F:F.490, F:F.490 Hydrogen bonds: F:R.96, F:T.402, F:T.402 Water bridges: F:S.84, F:R.96, F:R.404, F:R.404, F:K.431, F:N.486 Salt bridges: F:R.404, F:K.431 Metal complexes: F:H.383, F:H.491 HEC.70: 23 residues within 4Å: Chain D: N.141, W.142, Q.143 Chain F: V.371, H.372, N.375, V.377, D.381, C.382, P.403, M.407, A.410, C.411, C.414, H.415, W.418, A.423, A.426, I.427, I.430, F.490, P.493 Ligands: HEC.69 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain D, Hydrophobic interactions: F:V.371, F:V.377, F:P.403, F:W.418, F:I.427, F:I.430, F:F.490, D:W.142, D:Q.143 Water bridges: F:D.494, D:Q.143 Metal complexes: F:H.372, F:H.415 Hydrogen bonds: D:W.142, D:Q.143 HEC.71: 29 residues within 4Å: Chain F: A.11, C.14, F.15, H.18, I.21, H.25, H.30, V.33, N.34, C.35, H.37, C.38, H.39, T.59, R.60, M.61, I.193, L.194, F.228, P.233, H.234, R.239, F.274, R.276, R.282, I.284 Ligands: HEC.72, HEC.73, MRD.75 17 PLIP interactions: 17 interactions with chain F, Hydrophobic interactions: F:A.11, F:F.15, 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:H.234 Salt bridges: F:R.239, F:R.276, F:R.282, F:R.282 Metal complexes: F:H.39, F:H.234 HEC.72: 22 residues within 4Å: Chain E: H.37, T.68, C.69 Chain F: K.29, H.30, T.32, V.33, H.37, C.38, A.65, C.66, T.68, C.69, H.70, C.227, F.228, H.231, P.233, A.236 Ligands: HEC.60, HEC.67, HEC.71 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:K.29, F:K.29, F:T.68, F:H.231 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.73: 25 residues within 4Å: Chain F: V.9, Q.13, C.14, D.16, 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, G.277 Ligands: HEC.71 15 PLIP interactions: 15 interactions with chain F, Hydrophobic interactions: F:A.41, F:V.45, F:M.53, F:P.57 Water bridges: F:H.18, F:Q.275, F:R.276, F:R.276, F:R.278, F:R.278 Salt bridges: F:R.56, F:R.276 pi-Stacking: F:H.18 Metal complexes: F:H.18, F:H.44

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

MRD.10: 14 residues within 4Å: Chain A: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34 Chain B: P.8, N.34 Ligands: HEC.7, MRD.23 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.34 Water bridges: A:M.12, A:N.34 Hydrophobic interactions: B:P.8 MRD.11: 8 residues within 4Å: Chain A: R.56, P.57, V.58, T.59, M.61, L.194, D.195 Ligands: HEC.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.59 Water bridges: A:R.56, A:P.57, A:P.57 MRD.23: 15 residues within 4Å: Chain A: P.8, N.34 Chain B: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34, C.35 Ligands: MRD.10, HEC.19 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.11, A:P.8 Hydrogen bonds: B:V.9, B:A.11, B:N.34 Water bridges: B:N.34 MRD.24: 8 residues within 4Å: Chain B: Q.310, L.311, S.312, D.313, G.314, F.345, R.348, A.355 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.345 Water bridges: B:R.348 MRD.36: 14 residues within 4Å: Chain C: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34 Chain D: P.8, N.34 Ligands: HEC.33, MRD.49 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:P.8 Hydrogen bonds: C:N.34 Water bridges: C:M.12, C:N.34 MRD.37: 8 residues within 4Å: Chain C: R.56, P.57, V.58, T.59, M.61, L.194, D.195 Ligands: HEC.35 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.59 Water bridges: C:R.56, C:P.57, C:P.57 MRD.49: 15 residues within 4Å: Chain C: P.8, N.34 Chain D: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34, C.35 Ligands: MRD.36, HEC.45 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.11, C:P.8 Hydrogen bonds: D:V.9, D:A.11, D:N.34 Water bridges: D:N.34 MRD.50: 8 residues within 4Å: Chain D: Q.310, L.311, S.312, D.313, G.314, F.345, R.348, A.355 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.345 Water bridges: D:R.348 MRD.62: 14 residues within 4Å: Chain E: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34 Chain F: P.8, N.34 Ligands: HEC.59, MRD.75 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:P.8 Hydrogen bonds: E:N.34 Water bridges: E:M.12, E:N.34 MRD.63: 8 residues within 4Å: Chain E: R.56, P.57, V.58, T.59, M.61, L.194, D.195 Ligands: HEC.61 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.59 Water bridges: E:R.56, E:P.57, E:P.57 MRD.75: 15 residues within 4Å: Chain E: P.8, N.34 Chain F: P.8, V.9, D.10, A.11, M.12, H.25, A.31, T.32, V.33, N.34, C.35 Ligands: MRD.62, HEC.71 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:A.11, E:P.8 Hydrogen bonds: F:V.9, F:D.10, F:A.11, F:N.34 Water bridges: F:N.34 MRD.76: 8 residues within 4Å: Chain F: Q.310, L.311, S.312, D.313, G.314, F.345, R.348, A.355 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.345 Water bridges: F:R.348

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

MPD.12: 12 residues within 4Å: Chain A: R.87, V.128, D.130, F.137, Q.138, F.139, N.141, W.142, V.145 Chain E: Y.429, Y.433, R.497 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain A Hydrophobic interactions: E:Y.429, E:Y.433, A:F.139, A:W.142, A:W.142, A:W.142, A:V.145 Hydrogen bonds: A:R.87, A:R.87, A:F.139 Water bridges: A:V.128 MPD.25: 11 residues within 4Å: Chain B: R.87, V.128, D.130, Q.138, F.139, N.141, W.142, V.145 Chain D: Y.429, Y.433, R.497 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.139, B:W.142, B:W.142, B:V.145, D:Y.429, D:Y.433 Hydrogen bonds: B:R.87, B:R.87, B:F.139 Water bridges: B:V.128, B:F.137 MPD.26: 5 residues within 4Å: Chain B: Q.20, D.23, M.24, V.272, L.286 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.23, B:V.272 Water bridges: B:T.19, B:Q.20 MPD.38: 12 residues within 4Å: Chain A: Y.429, Y.433, R.497 Chain C: R.87, V.128, D.130, F.137, Q.138, F.139, N.141, W.142, V.145 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:Y.429, A:Y.433, C:F.139, C:W.142, C:W.142, C:W.142, C:V.145 Hydrogen bonds: C:R.87, C:R.87, C:F.139 Water bridges: C:V.128 MPD.51: 11 residues within 4Å: Chain D: R.87, V.128, D.130, Q.138, F.139, N.141, W.142, V.145 Chain F: Y.429, Y.433, R.497 11 PLIP interactions: 2 interactions with chain F, 9 interactions with chain D Hydrophobic interactions: F:Y.429, F:Y.433, D:F.139, D:W.142, D:W.142, D:V.145 Hydrogen bonds: D:R.87, D:R.87, D:F.139 Water bridges: D:V.128, D:F.137 MPD.52: 5 residues within 4Å: Chain D: Q.20, D.23, M.24, V.272, L.286 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:D.23, D:V.272 Water bridges: D:T.19, D:Q.20 MPD.64: 12 residues within 4Å: Chain C: Y.429, Y.433, R.497 Chain E: R.87, V.128, D.130, F.137, Q.138, F.139, N.141, W.142, V.145 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain E Hydrophobic interactions: C:Y.429, C:Y.433, E:F.139, E:W.142, E:W.142, E:W.142, E:V.145 Hydrogen bonds: E:R.87, E:R.87, E:F.139 Water bridges: E:V.128 MPD.77: 11 residues within 4Å: Chain B: Y.429, Y.433, R.497 Chain F: R.87, V.128, D.130, Q.138, F.139, N.141, W.142, V.145 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.139, F:W.142, F:W.142, F:V.145, B:Y.429, B:Y.433 Hydrogen bonds: F:R.87, F:R.87, F:F.139 Water bridges: F:V.128, F:F.137 MPD.78: 5 residues within 4Å: Chain F: Q.20, D.23, M.24, V.272, L.286 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:D.23, F:V.272 Water bridges: F:T.19, F:Q.20

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.22: 4 residues within 4Å: Chain B: S.49, S.50, R.51, R.52 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.49, B:S.50, B:S.50, B:S.50 Salt bridges: B:R.51 CIT.48: 4 residues within 4Å: Chain D: S.49, S.50, R.51, R.52 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.49, D:S.50, D:S.50, D:S.50 Salt bridges: D:R.51 CIT.74: 4 residues within 4Å: Chain F: S.49, S.50, R.51, R.52 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.49, F:S.50, F:S.50, F:S.50 Salt bridges: F:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polyakov, K.M. et al., High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. J.Mol.Biol. (2009)

Release Date

2008-04-08

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