SMTL ID : 4q1o.1

Free form of TvNiR, high dose data set

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 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.132, 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 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:P.116, 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:H.113, A:H.113, A:H.113, A:R.131, A:H.361 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.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, S.292, M.295, M.384, 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: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 Salt bridges: A:K.386 Metal complexes: A:H.231, A:H.398 HEC.3: 25 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 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:P.116, A:K.188, A:L.225, A:H.383 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.4: 24 residues within 4Å: Chain A: R.96, N.293, C.296, 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 20 PLIP interactions: 20 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 Hydrogen bonds: A:R.96, A:T.402, A:T.402 Water bridges: A:S.84, A:R.96, A:K.431, A:N.486 Salt bridges: A:R.404, A:K.431 Metal complexes: A:H.383, A:H.491 HEC.5: 18 residues within 4Å: Chain A: V.371, H.372, N.375, V.377, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Chain C: N.141, W.142, Q.143 Ligands: HEC.4 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.371, A:V.377, A:P.403, A:W.418, 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 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 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.11, A:F.15, 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:R.282 Salt bridges: A:R.239, A:R.276, A:R.282, A:R.282 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 10 PLIP interactions: 9 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, B:T.68 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 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.9, A:Q.13, A:H.39, A:A.41, A:V.45, A:A.48, A:M.53, A:P.57 Hydrogen bonds: A:G.277 Water bridges: A:R.276, 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.11: 23 residues within 4Å: Chain B: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.132, 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.13 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.116, B:V.129, B:A.132, 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: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 Metal complexes: H2O.23 HEC.12: 19 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, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.13, HEC.17 11 PLIP interactions: 11 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 Salt bridges: B:K.386 Metal complexes: B:H.231, B:H.398 HEC.13: 25 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.11, HEC.12, HEC.14 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.116, B:L.225, B:H.383 Hydrogen bonds: B:S.84, B:R.117, B:F.121 Water bridges: B:R.81, B:R.81, B:S.118, B:H.126, B:Q.400 Metal complexes: B:H.119, B:H.300 HEC.14: 24 residues within 4Å: Chain B: R.96, N.293, C.296, 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.13, HEC.15 19 PLIP interactions: 19 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 Water bridges: B:S.84, B:R.96, B:N.486 Salt bridges: B:R.404, B:K.431 Metal complexes: B:H.383, B:H.491 HEC.15: 17 residues within 4Å: Chain B: V.371, H.372, N.375, C.382, 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.14 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain F, Hydrophobic interactions: B:V.371, B:P.403, B:W.418, B:W.418, B:I.427, B:F.490, F:Q.143 Metal complexes: B:H.372, B:H.415 Hydrogen bonds: F:W.142 HEC.16: 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.17, HEC.18 18 PLIP interactions: 18 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 Metal complexes: B:H.39, B:H.234 HEC.17: 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.12, HEC.16 7 PLIP interactions: 7 interactions with chain B, Hydrophobic interactions: B:K.29, B:V.33, B:T.68 Salt bridges: B:K.29, B:K.29 Metal complexes: B:H.30, B:H.70 HEC.18: 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.16 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:Q.275, B:R.276, B:R.276 Salt bridges: B:R.56, B:R.276 Metal complexes: B:H.18, B:H.44 HEC.23: 23 residues within 4Å: Chain C: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.132, 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.25 22 PLIP interactions: 21 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:P.116, 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:H.113, C:A.114, C:R.131, C:H.361 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.46 HEC.24: 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, S.292, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.25, HEC.29 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:H.70, C:Q.73, 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 Salt bridges: C:K.386 Metal complexes: C:H.231, C:H.398 HEC.25: 25 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.23, HEC.24, HEC.26 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:P.116, C:K.188, C:L.225, C:H.383 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.26: 24 residues within 4Å: Chain C: R.96, N.293, C.296, 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.25, HEC.27 20 PLIP interactions: 20 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 Hydrogen bonds: C:R.96, C:T.402, C:T.402 Water bridges: C:S.84, C:R.96, C:K.431, C:N.486 Salt bridges: C:R.404, C:K.431 Metal complexes: C:H.383, C:H.491 HEC.27: 18 residues within 4Å: Chain C: V.371, H.372, N.375, V.377, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Chain E: N.141, W.142, Q.143 Ligands: HEC.26 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:V.371, C:V.377, C:P.403, C:W.418, 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 HEC.28: 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.29, HEC.30 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:A.11, C:F.15, 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:R.282 Salt bridges: C:R.239, C:R.276, C:R.282, C:R.282 Metal complexes: C:H.39, C:H.234 HEC.29: 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.24, HEC.28 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:K.29, C:K.29, C:V.33, C:T.68 Hydrogen bonds: C:A.236 Salt bridges: C:K.29, C:K.29 Metal complexes: C:H.30, C:H.70 HEC.30: 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.28 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:V.9, C:Q.13, C:H.39, C:A.41, C:V.45, C:A.48, C:M.53, C:P.57 Hydrogen bonds: C:G.277 Water bridges: C:R.276, 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.33: 23 residues within 4Å: Chain D: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.132, 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.35 20 PLIP interactions: 19 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:P.116, D:V.129, D:A.132, 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: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 Metal complexes: H2O.68 HEC.34: 19 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, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.35, HEC.39 11 PLIP interactions: 11 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 Salt bridges: D:K.386 Metal complexes: D:H.231, D:H.398 HEC.35: 25 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.33, HEC.34, HEC.36 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:P.116, D:L.225, 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:S.118, D:H.126, D:Q.400 Metal complexes: D:H.119, D:H.300 HEC.36: 24 residues within 4Å: Chain D: R.96, N.293, C.296, 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.35, HEC.37 20 PLIP interactions: 20 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:N.486 Salt bridges: D:R.404, D:K.431 Metal complexes: D:H.383, D:H.491 HEC.37: 17 residues within 4Å: Chain B: N.141, W.142, Q.143 Chain D: V.371, H.372, N.375, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Ligands: HEC.36 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain D, Hydrophobic interactions: B:Q.143, D:V.371, D:P.403, D:W.418, D:W.418, D:I.427, D:F.490 Hydrogen bonds: B:W.142 Metal complexes: D:H.372, D:H.415 HEC.38: 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.39, HEC.40 18 PLIP interactions: 18 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 Metal complexes: D:H.39, D:H.234 HEC.39: 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.34, HEC.38 7 PLIP interactions: 7 interactions with chain D, Hydrophobic interactions: D:K.29, D:V.33, D:T.68 Salt bridges: D:K.29, D:K.29 Metal complexes: D:H.30, D:H.70 HEC.40: 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.38 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:Q.275, D:R.276, D:R.276 Salt bridges: D:R.56, D:R.276 Metal complexes: D:H.18, D:H.44 HEC.45: 23 residues within 4Å: Chain E: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.132, 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.47 23 PLIP interactions: 22 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:P.116, 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:H.113, E:H.113, E:H.113, E:R.131, E:H.361 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.91 HEC.46: 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, S.292, M.295, M.384, Y.395, T.396, H.398 Ligands: HEC.47, HEC.51 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:H.70, E:Q.73, 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 Salt bridges: E:K.386 Metal complexes: E:H.231, E:H.398 HEC.47: 25 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.45, HEC.46, HEC.48 13 PLIP interactions: 13 interactions with chain E, Hydrophobic interactions: E:P.116, E:K.188, E:L.225, E:H.383 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.48: 24 residues within 4Å: Chain E: R.96, N.293, C.296, 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.47, HEC.49 19 PLIP interactions: 19 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 Hydrogen bonds: E:R.96, E:T.402 Water bridges: E:S.84, E:R.96, E:K.431, E:N.486 Salt bridges: E:R.404, E:K.431 Metal complexes: E:H.383, E:H.491 HEC.49: 18 residues within 4Å: Chain A: N.141, W.142, Q.143 Chain E: V.371, H.372, N.375, V.377, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Ligands: HEC.48 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.371, E:V.377, E:P.403, E:W.418, 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 HEC.50: 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.51, HEC.52 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:A.11, E:F.15, 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:R.282 Salt bridges: E:R.239, E:R.276, E:R.282, E:R.282 Metal complexes: E:H.39, E:H.234 HEC.51: 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.46, HEC.50 10 PLIP interactions: 1 interactions with chain F, 9 interactions with chain E, Hydrogen bonds: F:T.68, E:A.236 Hydrophobic interactions: E:K.29, E:K.29, E:V.33, E:T.68 Salt bridges: E:K.29, E:K.29 Metal complexes: E:H.30, E:H.70 HEC.52: 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.50 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:V.9, E:Q.13, E:H.39, E:A.41, E:V.45, E:A.48, E:M.53, E:P.57 Hydrogen bonds: E:G.277 Water bridges: E:R.276, 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.55: 23 residues within 4Å: Chain F: H.113, A.114, P.116, D.125, H.126, V.129, R.131, A.132, 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.57 21 PLIP interactions: 20 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:P.116, F:V.129, F:A.132, 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: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 Metal complexes: H2O.113 HEC.56: 19 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, S.292, M.295, M.384, K.386, Y.395, T.396, H.398 Ligands: HEC.57, HEC.61 11 PLIP interactions: 11 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 Salt bridges: F:K.386 Metal complexes: F:H.231, F:H.398 HEC.57: 25 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.55, HEC.56, HEC.58 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: F:P.116, F:L.225, 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:S.118, F:H.126, F:Q.400 Metal complexes: F:H.119, F:H.300 HEC.58: 24 residues within 4Å: Chain F: R.96, N.293, C.296, 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.57, HEC.59 19 PLIP interactions: 19 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 Water bridges: F:S.84, F:R.96, F:N.486 Salt bridges: F:R.404, F:K.431 Metal complexes: F:H.383, F:H.491 HEC.59: 17 residues within 4Å: Chain D: N.141, W.142, Q.143 Chain F: V.371, H.372, N.375, C.382, P.403, A.410, C.411, C.414, H.415, W.418, A.423, I.427, F.490 Ligands: HEC.58 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain D, Hydrophobic interactions: F:V.371, F:P.403, F:W.418, F:W.418, F:I.427, F:F.490, D:Q.143 Metal complexes: F:H.372, F:H.415 Hydrogen bonds: D:W.142 HEC.60: 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.61, HEC.62 18 PLIP interactions: 18 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 Metal complexes: F:H.39, F:H.234 HEC.61: 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.56, HEC.60 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:K.29, F:V.33, F:T.68 Salt bridges: F:K.29, F:K.29 Metal complexes: F:H.30, F:H.70 Water bridges: E:T.68 HEC.62: 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.60 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:Q.275, F:R.276, F:R.276 Salt bridges: F:R.56, F:R.276 Metal complexes: F:H.18, F:H.44

6 x CA: CALCIUM ION(Non-covalent)

CA.9: 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.3, H2O.11 CA.19: 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.25, H2O.25 CA.31: 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.48, H2O.56 CA.41: 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.70, H2O.70 CA.53: 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.101 CA.63: 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.115, H2O.116

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

MPD.10: 9 residues within 4Å: Chain A: R.87, V.128, Q.138, F.139, W.142, V.145 Chain E: Y.429, Y.433, R.497 10 PLIP interactions: 2 interactions with chain E, 8 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 MPD.20: 9 residues within 4Å: Chain B: R.87, V.128, Q.138, F.139, W.142, V.145 Chain D: Y.429, Y.433, R.497 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.139, B:W.142, 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 MPD.32: 9 residues within 4Å: Chain A: Y.429, Y.433, R.497 Chain C: R.87, V.128, Q.138, F.139, W.142, V.145 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.139, C:W.142, C:W.142, C:W.142, C:V.145, A:Y.429, A:Y.433 Hydrogen bonds: C:R.87, C:R.87, C:F.139 MPD.42: 9 residues within 4Å: Chain D: R.87, V.128, Q.138, F.139, W.142, V.145 Chain F: Y.429, Y.433, R.497 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain D Hydrophobic interactions: F:Y.429, F:Y.433, D:F.139, D:W.142, D:W.142, D:W.142, D:V.145 Hydrogen bonds: D:R.87, D:R.87, D:F.139 MPD.54: 9 residues within 4Å: Chain C: Y.429, Y.433, R.497 Chain E: R.87, V.128, Q.138, F.139, W.142, V.145 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:F.139, E:W.142, E:W.142, E:W.142, E:V.145, C:Y.429, C:Y.433 Hydrogen bonds: E:R.87, E:R.87, E:F.139 MPD.64: 9 residues within 4Å: Chain B: Y.429, Y.433, R.497 Chain F: R.87, V.128, Q.138, F.139, W.142, V.145 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain F Hydrophobic interactions: B:Y.429, B:Y.433, F:F.139, F:W.142, F:W.142, F:W.142, F:V.145 Hydrogen bonds: F:R.87, F:R.87, F:F.139

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 7 residues within 4Å: Chain B: Y.198, D.251, K.271, T.273, D.280, R.282, A.283 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.271, B:R.282 Water bridges: B:Y.198, B:Y.198, B:D.251 GOL.43: 7 residues within 4Å: Chain D: Y.198, D.251, K.271, T.273, D.280, R.282, A.283 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.271, D:R.282 Water bridges: D:Y.198, D:Y.198, D:D.201, D:R.322 GOL.65: 7 residues within 4Å: Chain F: Y.198, D.251, K.271, T.273, D.280, R.282, A.283 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.271, F:R.282 Water bridges: F:Y.198, F:Y.198, F:R.322

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

CIT.22: 3 residues within 4Å: Chain B: S.49, S.50, R.51 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.49, B:S.50, B:S.50 Salt bridges: B:R.51 CIT.44: 3 residues within 4Å: Chain D: S.49, S.50, R.51 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.49, D:S.50, D:S.50 Salt bridges: D:R.51 CIT.66: 3 residues within 4Å: Chain F: S.49, S.50, R.51 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:S.49, F:S.50, F:S.50 Salt bridges: F:R.51

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

2014-09-10

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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