SMTL ID : 2ein.1

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

2 x CU: COPPER (II) ION(Non-covalent)

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.34: 3 residues within 4Å: Chain N: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.7, H2O.7 MG.35: 3 residues within 4Å: Chain N: H.368, D.369 Chain O: E.198 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.22, H2O.28

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

NA.3: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43, A:D.442 NA.36: 4 residues within 4Å: Chain N: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:Q.43 Water bridges: N:Q.43, N:D.442

4 x HEA: HEME-A(Covalent)(Non-covalent)

HEA.4: 35 residues within 4Å: Chain A: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:I.37, A:A.62, A:M.65, A:I.66, A:V.374, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, A:S.382, A:Q.428, A:R.439, A:Y.440 Water bridges: A:R.438 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:H.378 Metal complexes: A:H.61, A:H.378 HEA.5: 32 residues within 4Å: Chain A: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, F.321, T.349, G.352, L.353, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain B: I.34, P.69, I.72, L.73 39 PLIP interactions: 36 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:T.309, A:A.313, A:T.316, A:F.321, A:F.321, A:T.349, A:L.353, A:I.356, A:I.356, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:H.291, A:T.316, A:D.369, A:D.369, A:R.439, A:R.439 Salt bridges: A:H.368, A:R.438 pi-Stacking: A:H.290 pi-Cation interactions: A:H.240, A:H.240, A:H.376 Metal complexes: A:H.376 HEA.39: 32 residues within 4Å: Chain N: A.24, G.27, M.28, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 31 PLIP interactions: 31 interactions with chain N, Hydrophobic interactions: N:T.31, N:V.58, N:A.62, N:M.65, N:V.70, N:V.374, N:F.377, N:L.381, N:V.386, N:V.386, N:T.424, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:R.38, N:Y.54, N:W.126, N:Y.371, N:S.382, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:H.378, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.40: 31 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, I.312, A.313, T.316, G.317, F.321, T.349, G.352, G.355, I.356, L.358, A.359, D.364, H.368, V.373, H.376, F.377, V.380, L.381, R.438 Chain O: I.34, P.69, I.72, L.73 37 PLIP interactions: 33 interactions with chain N, 4 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:T.309, N:A.313, N:T.316, N:F.321, N:T.349, N:I.356, N:I.356, N:L.358, N:L.358, N:V.373, N:V.373, N:F.377, N:F.377, N:V.380, N:L.381, N:L.381, O:I.34, O:I.34, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:H.291, N:H.291, N:T.316, N:D.369, N:D.369, N:R.438 Salt bridges: N:H.368, N:R.438 pi-Stacking: N:H.290 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

6 x TGL: TRISTEAROYLGLYCEROL(Non-covalent)

TGL.6: 16 residues within 4Å: Chain A: Y.379, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 15 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:N.422, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:W.450, B:L.7, B:L.28, B:V.31, B:F.32, B:F.32 Water bridges: B:L.7 Salt bridges: B:H.24, I:R.43 TGL.7: 24 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 17 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, A:W.334, A:W.334, A:L.342, A:K.411, A:F.414, A:F.414, A:F.418, D:W.78, D:V.81, D:V.81, D:I.89 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:E.77, D:W.78 TGL.32: 27 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, F.102, P.106, L.110, L.113, F.397, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29, S.31, A.35 27 PLIP interactions: 9 interactions with chain L, 18 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:L.27, L:F.28, L:F.28, L:F.29, L:F.29, L:A.35, A:T.17, A:L.18, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.81, A:F.102, A:P.106, A:L.110, A:L.113, A:F.397, A:F.400, A:I.472 TGL.41: 23 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain O: L.39, I.42, S.43, L.46, T.47, K.49 Chain Q: R.73, S.74, T.75, E.77, W.78, M.86, I.89 Chain V: R.16, H.20 16 PLIP interactions: 3 interactions with chain O, 9 interactions with chain N, 4 interactions with chain Q Hydrophobic interactions: O:L.39, O:I.42, O:L.46, N:W.334, N:W.334, N:L.342, N:K.411, N:F.414, N:A.415, N:F.418, N:F.418, Q:W.78, Q:I.89 Salt bridges: N:K.411 Hydrogen bonds: Q:E.77, Q:W.78 TGL.46: 17 residues within 4Å: Chain N: V.350, Y.379, N.422, F.426, P.427, H.429, F.430, L.433 Chain O: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain V: R.43 15 PLIP interactions: 9 interactions with chain N, 1 interactions with chain V, 5 interactions with chain O Hydrophobic interactions: N:V.350, N:N.422, N:F.426, N:F.426, N:F.426, N:P.427, N:H.429, N:F.430, N:F.430, O:L.28, O:V.31, O:F.32, O:F.32 Salt bridges: V:R.43, O:H.24 TGL.63: 25 residues within 4Å: Chain N: T.17, L.18, L.20, L.21, F.22, W.25, W.81, L.110, L.113, F.393, F.397, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, S.14, R.20, M.24, L.27, F.28, F.29, S.31, A.35 24 PLIP interactions: 15 interactions with chain N, 9 interactions with chain Y Hydrophobic interactions: N:T.17, N:L.18, N:L.20, N:L.21, N:L.21, N:W.25, N:W.25, N:W.25, N:W.25, N:W.81, N:L.113, N:F.393, N:F.397, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:L.27, Y:F.28, Y:F.28, Y:F.29, Y:F.29, Y:A.35

8 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)

PGV.8: 13 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 4 interactions with chain A, 4 interactions with chain M, 5 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, M:P.12, M:A.16, D:T.80, D:F.87, D:F.87, D:F.87, D:F.87, K:F.9 Hydrogen bonds: A:T.408 Water bridges: M:A.3, M:A.3 Salt bridges: K:H.10 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, V.155 Chain C: H.9, V.11, G.20, A.24, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, E.90, F.93 Ligands: PEK.17 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93, A:F.148, A:V.155, A:V.155 Hydrogen bonds: C:W.57, A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.19: 28 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, E.90, F.93, H.207, I.209, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Chain F: E.17 Ligands: PEK.17, CDL.21, ZN.25 28 PLIP interactions: 27 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:F.86, C:F.93, C:I.209, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, F:Q.12 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 12 residues within 4Å: Chain A: D.298 Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Chain P: W.258 Chain T: A.1 Ligands: CHD.16, CDL.61 6 PLIP interactions: 2 interactions with chain H, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: H:N.22 Water bridges: H:N.24, A:D.298, A:D.298 Hydrophobic interactions: C:W.99, C:W.99 PGV.42: 14 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 3 interactions with chain X, 3 interactions with chain Z, 3 interactions with chain Q, 6 interactions with chain N Hydrophobic interactions: X:F.9, X:F.9, Z:P.12, Z:A.16, Z:L.19, Q:T.80, Q:F.87, Q:F.87, N:T.408, N:W.409, N:W.409, N:I.412 Salt bridges: X:H.10 Hydrogen bonds: N:N.406, N:T.408 PGV.43: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, V.155 Chain P: H.9, G.20, A.24, M.27, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, E.90, F.93 Ligands: PEK.60 14 PLIP interactions: 8 interactions with chain N, 6 interactions with chain P Hydrophobic interactions: N:F.148, N:V.155, N:V.155, P:A.24, P:T.28, P:W.57, P:W.57, P:W.58, P:F.93 Hydrogen bonds: N:R.96, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.53: 23 residues within 4Å: Chain P: M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, E.90, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: CDL.55, PEK.60 24 PLIP interactions: 1 interactions with chain S, 23 interactions with chain P Water bridges: S:Q.12, P:S.65, P:R.221, P:H.231 Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:I.62, P:F.86, P:F.86, P:I.210, P:F.214, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:R.221, P:F.233, P:G.234 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.54: 12 residues within 4Å: Chain G: A.1 Chain N: F.237, D.298 Chain P: W.99, Y.102, H.103, L.106, A.107 Chain U: N.22, N.24 Ligands: CDL.27, CHD.51 9 PLIP interactions: 1 interactions with chain N, 3 interactions with chain P, 5 interactions with chain U Hydrophobic interactions: N:F.237, P:W.99, P:W.99 Salt bridges: P:H.103 Hydrogen bonds: U:N.22 Water bridges: U:N.24, U:N.24, U:N.24, U:R.27

14 x ZN: ZINC ION(Non-covalent)

ZN.10: 3 residues within 4Å: Chain B: H.22, H.26 Chain I: E.41 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.22, B:H.26 ZN.15: 3 residues within 4Å: Chain C: H.148, H.232, E.236 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.148, C:H.232, C:E.236, H2O.10 ZN.23: 1 residues within 4Å: Chain D: H.29 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.29 ZN.24: 5 residues within 4Å: Chain F: C.60, C.62, C.82, S.84, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85 ZN.25: 4 residues within 4Å: Chain C: H.231 Chain F: D.9, E.17 Ligands: PGV.19 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F Metal complexes: C:H.231, F:D.9, F:E.17 ZN.26: 2 residues within 4Å: Chain G: H.51 Chain H: E.78 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Metal complexes: G:H.51, H:E.78, H:E.78 ZN.31: 3 residues within 4Å: Chain A: H.503 Chain L: H.2, E.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain L Metal complexes: A:H.503, L:H.2, L:E.5, L:E.5 ZN.37: 4 residues within 4Å: Chain N: H.503, E.506 Chain Y: H.2 Ligands: ZN.38 3 PLIP interactions: 1 interactions with chain Y, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: Y:H.2, N:H.503, H2O.41 ZN.38: 3 residues within 4Å: Chain N: E.506 Chain P: H.3 Ligands: ZN.37 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain P Metal complexes: N:E.506, N:E.506, P:H.3 ZN.44: 3 residues within 4Å: Chain O: H.22, H.26 Chain V: E.41 2 PLIP interactions: 2 interactions with chain O Metal complexes: O:H.22, O:H.26 ZN.49: 3 residues within 4Å: Chain P: H.148, H.232, E.236 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.148, P:H.232, P:E.236, P:E.236, H2O.31 ZN.50: 3 residues within 4Å: Chain P: H.231 Chain S: D.9, E.17 3 PLIP interactions: 2 interactions with chain S, 1 interactions with chain P Metal complexes: S:D.9, S:E.17, P:H.231 ZN.57: 4 residues within 4Å: Chain S: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85 ZN.58: 2 residues within 4Å: Chain T: H.51 Chain U: E.78 3 PLIP interactions: 1 interactions with chain T, 2 interactions with chain U Metal complexes: T:H.51, U:E.78, U:E.78

2 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.11: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.161, B:C.196, B:C.196, B:E.198, B:C.200, B:C.200, B:H.204 CUA.45: 7 residues within 4Å: Chain O: H.161, C.196, E.198, I.199, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain O Metal complexes: O:H.161, O:C.196, O:C.196, O:E.198, O:C.200, O:C.200, O:H.204

2 x PSC: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE(Non-covalent)

PSC.12: 23 residues within 4Å: Chain A: F.268, F.321, L.324, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, W.65, L.68, P.69 Chain E: H.5, E.6, D.8, F.11, D.40, L.41 Chain I: R.10, A.14, L.17 20 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B, 3 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: A:F.268, A:F.321, A:F.321, A:F.321, A:L.324, A:H.328, B:I.41, B:M.56, B:V.61, B:W.65, B:W.65, B:W.65, B:L.68, B:P.69, I:A.14, I:L.17, I:L.17 Salt bridges: B:H.52, E:D.8 pi-Cation interactions: E:F.11 PSC.47: 23 residues within 4Å: Chain N: F.268, F.321, A.325, H.328 Chain O: I.41, H.52, T.55, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69 Chain R: H.5, E.6, D.8, F.11, D.40 Chain V: R.10, A.14, L.17 21 PLIP interactions: 11 interactions with chain O, 3 interactions with chain R, 5 interactions with chain N, 2 interactions with chain V Hydrophobic interactions: O:I.41, O:M.56, O:V.61, O:I.64, O:W.65, O:W.65, O:W.65, O:L.68, O:P.69, N:F.268, N:F.321, N:F.321, N:A.325, N:H.328, V:A.14, V:L.17 Hydrogen bonds: O:D.57 Salt bridges: O:H.52, R:H.5, R:D.8 pi-Cation interactions: R:F.11

8 x CHD: CHOLIC ACID(Non-covalent)

CHD.13: 12 residues within 4Å: Chain A: M.271, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.52 13 PLIP interactions: 7 interactions with chain T, 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: T:F.18, T:F.21, A:M.271, A:W.275, A:W.275, A:W.275 Water bridges: T:R.14, T:R.17, T:R.17 Salt bridges: T:R.14, T:R.17 Hydrogen bonds: B:E.62, B:T.63 CHD.16: 8 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.20, CDL.61 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:W.99, A:D.300, A:D.300, A:T.301 Salt bridges: C:H.103, A:H.233 Hydrophobic interactions: A:Y.304 CHD.22: 7 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164, L.223 Chain J: F.1 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: C:K.157, C:L.160, C:Q.161, C:F.164, C:F.164, C:L.223 Hydrogen bonds: C:Q.161, J:F.1 Salt bridges: C:R.156 CHD.28: 12 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, W.275 Chain O: Q.59, E.62, T.63, T.66 Ligands: PEK.18 12 PLIP interactions: 4 interactions with chain N, 5 interactions with chain G, 3 interactions with chain O Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, G:F.18 Water bridges: G:R.17, G:R.17 Salt bridges: G:R.14, G:R.17 Hydrogen bonds: O:Q.59, O:E.62, O:T.63 CHD.30: 8 residues within 4Å: Chain A: I.3, L.7, F.8 Chain J: Y.32, R.33, M.36, T.37, L.40 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain J Hydrophobic interactions: A:I.3, J:Y.32, J:R.33, J:M.36, J:L.40 Hydrogen bonds: J:R.33, J:R.33 CHD.51: 9 residues within 4Å: Chain N: H.233, D.300, T.301, Y.304, F.305 Chain P: W.99, H.103 Ligands: CDL.27, PGV.54 7 PLIP interactions: 4 interactions with chain N, 3 interactions with chain P Hydrophobic interactions: N:Y.304, N:F.305, P:W.99 Hydrogen bonds: N:T.301, P:W.99 Salt bridges: N:H.233, P:H.103 CHD.56: 6 residues within 4Å: Chain P: R.156, L.160, Q.161, F.164, L.223 Chain W: F.1 5 PLIP interactions: 4 interactions with chain P, 1 interactions with chain W Hydrophobic interactions: P:F.164, P:L.223 Hydrogen bonds: P:Q.161, W:F.1 Salt bridges: P:R.156 CHD.62: 6 residues within 4Å: Chain N: I.3 Chain W: Y.32, R.33, M.36, T.37, L.40 7 PLIP interactions: 6 interactions with chain W, 1 interactions with chain N Hydrophobic interactions: W:Y.32, W:R.33, W:M.36, W:L.40, N:I.3 Hydrogen bonds: W:R.33, W:R.33

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.14: 7 residues within 4Å: Chain C: W.34, M.40 Chain G: S.61, W.62, G.63, F.69 Ligands: PEK.17 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.61, G:G.63 DMU.33: 12 residues within 4Å: Chain A: L.35, F.459 Chain D: L.95, W.98, Y.102 Chain M: L.27, L.28, A.30, G.31, W.32, Y.35, H.36 11 PLIP interactions: 3 interactions with chain M, 2 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: M:L.27, M:A.30, A:L.35, A:F.459, D:L.95, D:W.98, D:W.98, D:W.98 Hydrogen bonds: M:Y.35, D:Y.102, D:Y.102 DMU.48: 6 residues within 4Å: Chain P: W.34, M.40 Chain T: S.61, W.62, G.63 Ligands: PEK.60 2 PLIP interactions: 2 interactions with chain T Hydrogen bonds: T:S.61, T:G.63 DMU.64: 12 residues within 4Å: Chain N: F.459, L.462 Chain Q: L.95, W.98, Y.102 Chain Z: L.27, L.28, G.31, W.32, L.34, Y.35, H.36 11 PLIP interactions: 2 interactions with chain N, 6 interactions with chain Q, 3 interactions with chain Z Hydrophobic interactions: N:F.459, N:L.462, Q:L.95, Q:W.98, Q:W.98, Z:L.27, Z:L.27, Z:L.34 Hydrogen bonds: Q:Y.102, Q:Y.102, Q:Y.102

6 x PEK: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(Non-covalent)

PEK.17: 23 residues within 4Å: Chain A: H.151, V.155, L.215 Chain C: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.9, DMU.14, PGV.19 12 PLIP interactions: 4 interactions with chain C, 6 interactions with chain G, 2 interactions with chain A Hydrophobic interactions: C:W.34, C:F.203, G:F.69, A:V.155, A:L.215 Hydrogen bonds: C:Y.181, C:I.188, G:T.68, G:F.70, G:N.76 Water bridges: G:F.69, G:F.69 PEK.18: 20 residues within 4Å: Chain C: K.157, H.158, Q.161, I.165, T.168, L.169, Y.172 Chain F: A.1 Chain G: K.5, R.17, F.21, G.22, L.23, L.25 Chain N: W.275, S.279 Chain O: Q.59, T.66 Ligands: CDL.27, CHD.28 17 PLIP interactions: 1 interactions with chain F, 7 interactions with chain G, 2 interactions with chain O, 6 interactions with chain C, 1 interactions with chain N Hydrogen bonds: F:A.1, G:R.17, O:Q.59, C:K.157, C:K.157 Hydrophobic interactions: G:F.21, G:F.21, G:L.23, G:L.25, O:T.66, C:I.165, C:L.169, C:Y.172, N:W.275 Salt bridges: G:R.17, G:R.17 Water bridges: C:Q.161 PEK.29: 19 residues within 4Å: Chain G: S.2, A.3, K.5, G.6, H.8 Chain N: V.193 Chain P: K.77, R.80, Y.81, I.84, L.85, T.95, F.98, W.240, F.244, V.247, V.248, F.251 Ligands: CDL.27 14 PLIP interactions: 9 interactions with chain P, 1 interactions with chain N, 4 interactions with chain G Hydrophobic interactions: P:Y.81, P:L.85, P:F.98, P:W.240, P:F.244, P:V.247, P:V.248, P:F.251, N:V.193, G:A.3, G:K.5, G:K.5, G:K.5 Salt bridges: P:K.77 PEK.52: 17 residues within 4Å: Chain A: W.275, S.279, I.314 Chain B: Q.59, T.66 Chain P: K.157, H.158, Q.161, T.168, Y.172 Chain S: A.1 Chain T: R.17, F.21, G.22, L.23 Ligands: CHD.13, CDL.61 11 PLIP interactions: 3 interactions with chain P, 4 interactions with chain T, 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain S Hydrophobic interactions: P:Y.172, T:F.21, T:L.23, B:T.66, A:W.275, A:I.314 Hydrogen bonds: P:H.158, T:R.17, S:A.1 Water bridges: P:Q.161 Salt bridges: T:R.17 PEK.59: 17 residues within 4Å: Chain C: K.77, R.80, Y.81, I.84, L.85, T.95, F.98, W.240, F.244, V.247, V.248, F.251 Chain T: S.2, A.3, K.5, G.6, H.8 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain T Hydrophobic interactions: C:Y.81, C:I.84, C:I.84, C:L.85, C:F.98, C:F.244, C:V.247, C:V.248, C:F.251, T:A.3, T:K.5, T:K.5, T:K.5 Water bridges: C:K.77, C:K.77 Salt bridges: C:K.77, C:R.80 PEK.60: 23 residues within 4Å: Chain N: H.151, L.210, L.215 Chain P: W.34, Y.181, Y.182, A.184, F.186, T.187, I.188, F.198, G.202, F.203, G.205 Chain T: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.43, DMU.48, PGV.53 14 PLIP interactions: 2 interactions with chain N, 7 interactions with chain T, 5 interactions with chain P Hydrophobic interactions: N:L.210, N:L.215, T:W.62, T:F.69, P:W.34, P:Y.181, P:F.203 Hydrogen bonds: T:T.68, T:F.70, T:N.76, P:Y.181, P:I.188 Water bridges: T:F.69, T:F.69

4 x CDL: CARDIOLIPIN(Non-covalent)

CDL.21: 26 residues within 4Å: Chain C: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, V.171, T.174, I.209, S.212, T.213, I.216, V.217, F.220, R.221, K.224, H.226 Chain J: K.8, F.12, T.27, D.28 Ligands: PGV.19 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain J Hydrophobic interactions: C:T.48, C:M.51, C:L.52, C:M.54, C:Y.55, C:W.58, C:W.58, C:I.62, C:V.171, C:T.174, C:I.209, C:T.213, C:I.216, C:F.220 Hydrogen bonds: C:Y.55, C:R.59, J:D.28 Water bridges: C:R.59, C:R.59 Salt bridges: C:R.63, C:K.224, C:K.224, C:H.226, J:K.8, J:K.8 CDL.27: 29 residues within 4Å: Chain C: L.127, L.131, T.134, L.138, L.250 Chain G: L.23, S.27, L.30, C.31, N.34, L.37, H.38, R.42 Chain N: F.282, I.286, D.300, Y.304, S.307, I.311 Chain O: I.74, A.77, L.78, L.81, R.82, Y.85 Ligands: PEK.18, PEK.29, CHD.51, PGV.54 22 PLIP interactions: 9 interactions with chain G, 5 interactions with chain O, 4 interactions with chain N, 4 interactions with chain C Hydrophobic interactions: G:L.23, G:L.30, G:L.30, G:L.30, G:L.37, O:I.74, O:I.74, O:A.77, O:L.78, O:L.81, N:F.282, N:F.282, N:I.286, N:Y.304, C:T.134, C:L.138, C:L.138, C:L.250 Hydrogen bonds: G:N.34, G:R.42 Salt bridges: G:H.38, G:H.38 CDL.55: 22 residues within 4Å: Chain P: T.48, M.51, L.52, M.54, Y.55, W.58, R.59, I.62, R.63, F.67, I.209, T.213, V.217, F.220, K.224, H.226 Chain W: K.8, F.12, T.27, D.28, L.31 Ligands: PGV.53 25 PLIP interactions: 18 interactions with chain P, 7 interactions with chain W Hydrophobic interactions: P:T.48, P:M.51, P:L.52, P:M.54, P:Y.55, P:Y.55, P:W.58, P:I.209, P:I.209, P:T.213, W:L.31, W:L.31 Hydrogen bonds: P:Y.55, P:R.59, W:D.28 Water bridges: P:R.59, P:K.224, W:K.8, W:K.8 Salt bridges: P:R.63, P:K.224, P:K.224, P:H.226, W:K.8, W:K.8 CDL.61: 32 residues within 4Å: Chain A: F.282, I.286, D.300, Y.304, S.307, I.311 Chain B: I.74, A.77, L.78, L.81, R.82, Y.85 Chain P: L.127, L.131, T.134, S.135, L.138, V.142, L.250, Y.253 Chain T: L.23, S.27, L.30, C.31, L.33, N.34, L.37, H.38, R.42 Ligands: CHD.16, PGV.20, PEK.52 27 PLIP interactions: 10 interactions with chain T, 7 interactions with chain P, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: T:L.23, T:L.30, T:L.30, T:L.30, T:L.33, T:L.37, P:L.131, P:T.134, P:L.138, P:V.142, P:L.250, P:Y.253, A:F.282, A:F.282, A:I.286, A:Y.304, A:I.311, B:I.74, B:I.74, B:A.77, B:L.81 Hydrogen bonds: T:N.34, P:N.125 Salt bridges: T:H.38, T:H.38, T:R.42 Water bridges: A:S.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muramoto, K. et al., A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-05-29

Peptides

Cytochrome c oxidase subunit 1: AN
Cytochrome c oxidase subunit 2: BO
Cytochrome c oxidase subunit 3: CP
Cytochrome c oxidase subunit 4 isoform 1: DQ
Cytochrome c oxidase polypeptide Va: ER
Cytochrome c oxidase polypeptide Vb: FS
Cytochrome c oxidase polypeptide VIa-heart: GT
Cytochrome c oxidase subunit VIb isoform 1: HU
Cytochrome c oxidase polypeptide VIc: IV
Cytochrome c oxidase polypeptide VIIa-heart: JW
Cytochrome c oxidase polypeptide VIIb: KX
Cytochrome c oxidase polypeptide VIIc: LY
Cytochrome c oxidase polypeptide VIII-heart: MZ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N
N

B
B

O
O

C
C

P
P

D
D

Q
Q

E
E

R
R

F
F

S
S

G
G

T
T

H
H

U
U

I
I

V
V

J
J

W
W

K
K

X
X

L
L

Y
Y

M
M

Z
Z

Membrane

We predict this structure to be a membrane protein.
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Cytochrome c oxidase subunit 1

Cytochrome c oxidase subunit 2

Cytochrome c oxidase subunit 3

Cytochrome c oxidase subunit 4 isoform 1

Cytochrome c oxidase polypeptide Va

Cytochrome c oxidase polypeptide Vb

Cytochrome c oxidase polypeptide VIa-heart

Cytochrome c oxidase subunit VIb isoform 1

Cytochrome c oxidase polypeptide VIc

Cytochrome c oxidase polypeptide VIIa-heart

Cytochrome c oxidase polypeptide VIIb

Cytochrome c oxidase polypeptide VIIc

Cytochrome c oxidase polypeptide VIII-heart

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