SMTL ID : 2e84.1

Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F) in the presence of zinc ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: E.415, D.419 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.415, A:E.415, A:D.419 ZN.2: 3 residues within 4Å: Chain A: H.534, E.540, E.549 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.534, A:E.540, A:E.540, A:E.549, A:E.549 ZN.3: 1 residues within 4Å: Chain A: E.442 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.442, A:E.442 ZN.4: 5 residues within 4Å: Chain A: H.320, K.323, I.324, D.325, N.326 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.320, A:K.323, A:D.325, H2O.2

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: K.523, H.527 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.527 NA.6: 1 residues within 4Å: Chain A: E.124 No protein-ligand interaction detected (PLIP) NA.7: 1 residues within 4Å: Chain A: D.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.136 NA.8: 2 residues within 4Å: Chain A: M.279 Ligands: HEM.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.279 Water bridges: A:L.281, A:K.414, A:K.414, A:R.417, A:R.417

16 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.9: 22 residues within 4Å: Chain A: V.46, I.48, F.64, H.66, H.69, V.73, E.82, C.83, C.86, H.87, M.95, L.97, K.98, F.99, R.101, Y.114, R.221, H.225, I.229, V.247 Ligands: HEM.10, HEM.15 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:V.46, A:F.64, A:H.69, A:V.73, A:L.97, A:H.225, A:I.229, A:I.229, A:V.247 Hydrogen bonds: A:F.99, A:Y.114 Salt bridges: A:R.101, A:R.221, A:H.225 pi-Stacking: A:H.66, A:H.66, A:H.87, A:H.87 pi-Cation interactions: A:H.87 Metal complexes: A:H.66, A:H.87 HEM.10: 21 residues within 4Å: Chain A: V.62, T.63, F.64, R.68, H.69, A.72, V.73, T.85, F.99, Y.114, N.117, C.118, C.121, H.122, Q.125, K.131, T.132, G.133, P.134 Ligands: HEM.9, HEM.11 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.62, A:A.72, A:V.73, A:T.85, A:F.99, A:Y.114 Water bridges: A:R.68 Salt bridges: A:R.68, A:R.68, A:K.131, A:K.131 pi-Stacking: A:F.64, A:H.69, A:H.69, A:H.122, A:H.122 pi-Cation interactions: A:H.69, A:H.122 Metal complexes: A:H.69, A:H.122 HEM.11: 22 residues within 4Å: Chain A: I.48, G.49, V.50, M.51, L.57, E.58, L.59, V.62, K.111, Y.114, H.115, C.118, I.119, H.122, P.134, Q.135, D.136, E.138, C.139, C.142, H.143 Ligands: HEM.10 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:I.48, A:M.51, A:L.57, A:V.62, A:Y.114, A:Y.114, A:Y.114, A:I.119, A:P.134 Hydrogen bonds: A:M.51, A:E.58, A:L.59 pi-Stacking: A:H.115, A:H.115, A:H.143, A:H.143 pi-Cation interactions: A:H.115 Metal complexes: A:H.115, A:H.143 HEM.12: 21 residues within 4Å: Chain A: G.156, L.157, H.162, H.165, V.166, I.171, N.180, C.181, C.184, H.185, E.202, S.204, C.205, L.270, E.271, T.315, C.316, R.317, I.324 Ligands: HEM.13, HEM.14 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:L.157, A:H.165, A:V.166, A:I.171, A:N.180, A:E.202, A:L.270, A:L.270, A:I.324 Hydrogen bonds: A:L.157, A:C.316, A:R.317 Salt bridges: A:R.206 pi-Stacking: A:H.162, A:H.162, A:H.185, A:H.185, A:H.185 pi-Cation interactions: A:H.162 Metal complexes: A:H.162, A:H.185 HEM.13: 18 residues within 4Å: Chain A: K.94, C.184, H.185, H.186, Y.188, L.195, D.203, S.204, C.205, C.208, H.209, K.216, K.217, P.218, A.223, T.226, Q.227 Ligands: HEM.12 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:Y.188, A:L.195, A:L.195, A:D.203, A:K.217, A:P.218, A:A.223, A:T.226, A:Q.227 Salt bridges: A:K.94, A:K.216 pi-Stacking: A:H.186, A:H.186, A:H.209, A:H.209, A:H.209 Metal complexes: A:H.186, A:H.209 HEM.14: 21 residues within 4Å: Chain A: I.155, L.157, L.161, R.164, H.165, A.168, A.170, I.171, A.183, C.184, Q.227, C.228, C.231, H.232, D.243, S.244, G.245, P.246, F.261 Ligands: HEM.12, HEM.15 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:I.155, A:L.157, A:L.161, A:L.161, A:A.168, A:A.170, A:I.171, A:I.171, A:A.183, A:Q.227, A:F.261, A:F.261 Water bridges: A:R.164, A:R.164, A:D.243, A:D.243 Salt bridges: A:R.164, A:R.164, A:K.262 pi-Stacking: A:H.165, A:H.165, A:H.232, A:H.232 Metal complexes: A:H.165, A:H.232 HEM.15: 21 residues within 4Å: Chain A: V.46, H.66, W.152, Q.154, I.155, R.206, L.220, R.221, A.224, H.225, C.228, I.229, H.232, P.246, V.247, S.248, C.249, C.252, H.253 Ligands: HEM.9, HEM.14 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:V.46, A:W.152, A:Q.154, A:R.221, A:A.224, A:I.229 Hydrogen bonds: A:Q.154 Salt bridges: A:R.206 pi-Stacking: A:W.152, A:W.152, A:W.152, A:H.225, A:H.225, A:H.253, A:H.253 Metal complexes: A:H.225, A:H.253 HEM.16: 21 residues within 4Å: Chain A: R.272, Q.274, P.275, M.279, V.280, F.304, H.306, H.309, S.313, T.315, C.316, C.319, H.320, I.324, D.325, N.326, C.327, T.328, K.414 Ligands: NA.8, HEM.18 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:Q.274, A:Q.274, A:F.304, A:H.309, A:I.324, A:I.324 Hydrogen bonds: A:N.326, A:C.327, A:T.328 Water bridges: A:R.272, A:L.281, A:K.414, A:R.417 Salt bridges: A:K.414 pi-Stacking: A:H.306, A:H.306, A:H.320, A:H.320, A:H.320 pi-Cation interactions: A:H.320 Metal complexes: A:H.306, A:H.320 HEM.17: 17 residues within 4Å: Chain A: C.319, H.320, H.321, V.322, K.323, N.326, C.327, C.330, H.331, D.338, G.339, N.340, V.342, A.347, S.353, K.355, S.356 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:V.322, A:A.347 Salt bridges: A:K.355, A:K.355 pi-Stacking: A:H.321, A:H.321, A:H.331, A:H.331, A:H.331 pi-Cation interactions: A:K.355 Metal complexes: A:H.321, A:H.331 HEM.18: 21 residues within 4Å: Chain A: V.302, F.304, N.305, V.308, H.309, A.312, C.319, M.354, K.355, S.356, C.357, C.360, H.361, K.364, C.392, R.428, K.475, L.476, T.479 Ligands: HEM.16, HEM.20 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.302, A:A.312, A:K.364, A:L.476 Hydrogen bonds: A:N.305, A:K.475 Salt bridges: A:R.428, A:K.475 pi-Stacking: A:F.304, A:H.309, A:H.309, A:H.361, A:H.361 Metal complexes: A:H.309, A:H.361 HEM.19: 21 residues within 4Å: Chain A: V.365, A.369, C.370, C.373, H.374, M.377, T.379, Q.384, P.385, A.388, L.467, I.471, D.474, L.476, A.477, F.480, H.481, T.486, V.487, A.489, G.490 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.467, A:I.471, A:I.471, A:D.474, A:L.476, A:L.476, A:A.477, A:F.480, A:F.480, A:F.480, A:T.486, A:V.487, A:A.489 Hydrogen bonds: A:Q.384 Salt bridges: A:K.382 pi-Stacking: A:H.374, A:H.374, A:H.481, A:H.481 pi-Cation interactions: A:H.481 Metal complexes: A:H.374, A:H.481 HEM.20: 21 residues within 4Å: Chain A: V.280, L.281, P.282, G.297, A.298, M.299, P.301, V.302, I.344, M.348, H.349, C.357, H.361, Q.384, P.385, A.388, C.389, C.392, H.393, F.480 Ligands: HEM.18 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.280, A:V.302, A:V.302, A:I.344, A:M.348, A:F.480 Hydrogen bonds: A:A.298, A:M.299, A:K.300 Salt bridges: A:H.393 pi-Stacking: A:H.349, A:H.349, A:H.393, A:H.393 Metal complexes: A:H.349, A:H.393 HEM.21: 21 residues within 4Å: Chain A: T.434, L.435, D.439, I.440, P.441, V.444, I.446, L.458, H.460, I.463, V.464, V.487, C.488, C.491, H.492, K.499, P.501, K.503, C.504, Y.526 Ligands: HEM.23 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:L.435, A:I.440, A:P.441, A:L.458, A:I.463, A:V.464 Hydrogen bonds: A:C.504, A:Y.526 pi-Stacking: A:H.460, A:H.460, A:H.492, A:H.492 Metal complexes: A:H.460, A:H.492 HEM.22: 17 residues within 4Å: Chain A: F.376, K.378, C.491, H.492, H.493, N.494, S.495, P.502, K.503, C.504, C.507, H.508, D.518, P.520, A.525, Q.528, Q.529 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:F.376, A:P.502, A:P.520, A:A.525, A:Q.528, A:Q.529 Hydrogen bonds: A:N.494 Water bridges: A:F.376 Salt bridges: A:K.378, A:H.493 pi-Stacking: A:H.493, A:H.493, A:H.508, A:H.508 Metal complexes: A:H.493, A:H.508 HEM.23: 19 residues within 4Å: Chain A: C.373, I.446, L.458, P.459, K.462, I.463, T.466, L.467, C.491, Q.529, C.530, C.533, H.534, M.537, L.539, E.549, C.550 Ligands: HEM.21, HEM.24 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:I.446, A:L.458, A:P.459, A:I.463, A:T.466, A:L.467, A:Q.529, A:L.539 Hydrogen bonds: A:T.466, A:T.466 Water bridges: A:K.462, A:K.462 Salt bridges: A:K.462 pi-Stacking: A:H.534 pi-Cation interactions: A:H.534 Metal complexes: A:H.534 HEM.24: 20 residues within 4Å: Chain A: I.446, G.447, V.448, L.449, S.450, D.451, K.452, Y.453, S.456, K.523, Y.526, H.527, C.530, M.531, H.534, C.547, E.549, C.550, H.551 Ligands: HEM.23 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:I.446, A:L.449, A:Y.453, A:Y.526, A:Y.526, A:Y.526 Hydrogen bonds: A:L.449, A:S.450, A:D.451, A:K.452, A:Y.453 Water bridges: A:D.451 pi-Stacking: A:H.527, A:H.527, A:H.551, A:H.551 pi-Cation interactions: A:K.523, A:H.551 Metal complexes: A:H.527, A:H.551

Links

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Citation

Osuka, H. et al., Structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris (Miyazaki F). To be Published

Release Date

2008-01-15

Peptides

High-molecular-weight cytochrome c: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

High-molecular-weight cytochrome c