SMTL ID : 7vvr.2 (1 other biounit)

Bovine cytochrome c oxidese in CN-bound mixed valence state at 50 K

HEA.1: 34 residues within 4Å: Chain A: A.24, G.27, T.31, S.34, I.37, R.38, Y.54, V.58, H.61, A.62, M.65, I.66, M.69, V.70, G.125, W.126, Y.371, F.377, H.378, L.381, S.382, V.386, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: TGL.70 33 PLIP interactions: 33 interactions with chain A, Hydrophobic interactions: A:T.31, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:F.377, A:L.381, A:L.381, 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, A:R.438, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.2: 33 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, V.320, 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 Ligands: CYN.6 39 PLIP interactions: 34 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:L.353, A:I.356, A:I.356, A:L.358, A:L.358, 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.34, B:P.69, 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.438 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.240 Metal complexes: A:H.376

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CYN.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.13, H2O.14, H2O.16

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:Q.43

CYN.6: 7 residues within 4Å: Chain A: H.240, V.243, H.290, H.291, H.376 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP)

TGL.7: 15 residues within 4Å: Chain A: V.350, T.354, Y.379, N.422, F.426, H.429, F.430, L.433 Chain B: L.7, G.8, L.28, V.31, F.32, S.35 Chain I: R.43 14 PLIP interactions: 5 interactions with chain A, 2 interactions with chain I, 7 interactions with chain B Hydrophobic interactions: A:V.350, A:T.354, A:F.426, A:H.429, A:F.430, B:L.7, B:V.31, B:F.32, B:F.32 Water bridges: I:R.43, B:G.8, B:F.9 Salt bridges: I:R.43, B:H.24 TGL.49: 19 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, F.414, A.415, V.419 Chain B: L.39, I.42, S.43, T.47 Chain D: R.70, E.74, W.75, V.78, M.83, I.86 Chain I: R.16 Ligands: EDO.17 12 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:A.415, A:V.419, D:V.78, B:L.39, B:I.42, B:T.47 Salt bridges: A:K.411 Hydrogen bonds: D:T.72, D:E.74 TGL.70: 26 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, P.106, F.109, L.110, L.113, F.393, F.400, S.401, I.472 Chain L: I.10, P.11, F.12, R.19, M.23, M.24, F.27, F.28, I.38 Ligands: HEA.1 23 PLIP interactions: 14 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:F.2, A:T.17, A:L.18, A:L.20, A:L.21, A:F.22, A:W.25, A:W.25, A:W.81, A:F.109, A:F.109, A:L.113, A:F.400, A:I.472, L:I.10, L:F.12, L:F.12, L:M.23, L:F.27, L:F.27, L:F.28, L:F.28, L:I.38

PGV.8: 10 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15 17 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D, 5 interactions with chain K, 3 interactions with chain M Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, D:A.81, D:F.84, D:F.84, D:F.84, K:F.4, K:F.4, K:F.4, M:P.12, M:P.12 Hydrogen bonds: A:T.408 Water bridges: K:F.4, M:A.3 Salt bridges: K:H.5 PGV.9: 27 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, P.200 Chain C: H.7, V.9, G.18, A.22, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, E.88, F.91 Ligands: PEK.35 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:F.148, A:P.200, C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.91 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.37: 26 residues within 4Å: Chain C: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, F.91, F.201, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: CDL.39 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.56, C:W.56, C:W.56, C:W.56, C:W.56, C:I.60, C:F.84, C:F.91, C:F.201, C:I.208, C:I.208, C:I.208, C:T.211, C:F.212, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Water bridges: C:S.63, C:Q.74, C:R.219, C:H.229, C:H.229, F:Q.12, F:E.17 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.38: 12 residues within 4Å: Chain A: F.237, D.298 Chain C: V.89, T.93, W.97, Y.100, H.101, L.104, A.105 Chain H: N.16, N.18 Ligands: CHD.33 12 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C, 5 interactions with chain H Hydrophobic interactions: A:F.237, C:V.89, C:T.93, C:W.97, C:W.97, C:W.97 Hydrogen bonds: A:D.298, H:N.16 Water bridges: H:N.18, H:N.18, H:N.18, H:N.18

EDO.10: 7 residues within 4Å: Chain A: Y.19, M.71, P.72, S.101, L.105, S.156, S.157 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligands: EDO.22 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, V.485, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: L.483, T.484, V.485, T.488, W.494, G.497, C.498 Chain D: Y.8 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain A: R.5, N.11, K.13, D.14, W.81, P.499, P.500, Y.502 Chain L: N.9 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.59 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: E.507 Chain C: T.3 Chain F: P.30, N.32, P.50, R.56 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: W.24 Ligands: TGL.49 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: E.62 Ligands: CHD.25 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: K.333, W.334, S.335, P.336, D.407, K.411 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: P.131, D.221, P.222 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: L.136, A.137 Chain B: Q.103 Ligands: EDO.11 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: N.496, T.504, F.505, E.506, E.507 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: P.106, L.110 Chain C: L.20 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain B: L.135, F.206 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain B: E.157 Ligands: EDO.44 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: Y.447 Chain B: M.1, A.2, Q.10, L.136, P.166, Y.193 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: Q.103, W.104, Y.105, Y.121, N.203 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: G.177 Chain C: E.109 Chain H: W.62, W.66 Ligands: EDO.44 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain C: G.139, T.143, H.241 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain C: N.10, P.11 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.44: 7 residues within 4Å: Chain A: P.222, A.223 Chain B: G.177 Chain C: E.109 Chain H: W.62 Ligands: EDO.28, EDO.31 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain C: H.1, Q.2, H.68 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain C: L.125, Y.251, W.256 Ligands: CDL.62 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain C: W.144, S.148, H.156 Chain F: S.2 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain D: K.118, L.121, D.122, W.135, N.140 Chain K: P.45 Ligand excluded by PLIP EDO.51: 6 residues within 4Å: Chain D: Y.19, D.23 Chain E: W.23, R.26, K.27, N.30 Ligand excluded by PLIP EDO.52: 7 residues within 4Å: Chain A: L.495 Chain D: Y.8, A.9, L.10, P.11 Chain F: F.72, W.73 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain E: Y.14, K.17, E.24 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain E: R.49, R.52, R.53, L.92 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain A: Y.510 Chain F: P.36, K.37, T.39, N.47, L.48 Ligand excluded by PLIP EDO.58: 6 residues within 4Å: Chain C: P.71, Q.74, N.228, H.229 Chain F: D.9, E.17 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain A: T.489, T.490 Chain F: S.67, T.68, V.69, W.71 Ligands: EDO.15 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain F: F.72, Q.80, R.81 Ligand excluded by PLIP EDO.63: 2 residues within 4Å: Chain G: A.1, A.3 Ligand excluded by PLIP EDO.64: 6 residues within 4Å: Chain C: G.118 Chain G: A.46, F.47, I.48, L.53, R.54 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain H: D.29, R.32, C.33, Y.50 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain J: A.6, Q.9, K.10, Q.13 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain A: L.113, M.117 Chain L: I.38 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain L: G.7, K.8, I.10, F.12, S.13 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain A: T.46, L.47 Chain D: V.100 Chain M: D.38, K.41 Ligand excluded by PLIP

CHD.25: 7 residues within 4Å: Chain A: M.271, G.272, W.275 Chain B: E.62, T.63, T.66 Ligands: EDO.19 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.66, A:M.271, A:W.275, A:W.275, A:W.275 Hydrogen bonds: B:E.62, B:T.63 CHD.33: 8 residues within 4Å: Chain A: H.233, W.288, D.300, T.301, Y.304 Chain C: W.97, H.101 Ligands: PGV.38 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:W.288, A:Y.304, A:Y.304, C:W.97 Hydrogen bonds: A:T.301, C:W.97 Water bridges: A:D.300, A:T.301 Salt bridges: A:H.233, C:H.101 CHD.40: 7 residues within 4Å: Chain C: R.154, L.158, Q.159, F.162, F.217, L.221 Chain J: F.1 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain J Hydrophobic interactions: C:L.158, C:F.162, C:F.162, C:F.162, C:F.217, C:L.221, J:F.1 Salt bridges: C:R.154 Hydrogen bonds: J:F.1 CHD.68: 7 residues within 4Å: Chain A: I.3, L.7 Chain J: Y.32, R.33, M.36, T.37, L.40 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain A Hydrophobic interactions: J:Y.32, J:R.33, A:I.3 Hydrogen bonds: J:R.33 CHD.73: 6 residues within 4Å: Chain L: W.18, L.21, A.22 Chain M: E.14, I.17, V.21 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:I.17 Hydrogen bonds: M:E.14

CUA.26: 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

DMU.32: 4 residues within 4Å: Chain B: H.26, I.30, L.33 Chain I: K.36 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain B Hydrogen bonds: I:K.36, I:K.36 Hydrophobic interactions: B:L.33 Salt bridges: B:H.26 DMU.41: 13 residues within 4Å: Chain A: L.110, A.114, L.145 Chain C: S.27, M.31, F.35 Chain J: Y.45, S.46, Y.48, C.49, W.52, K.58 Ligands: DMU.48 11 PLIP interactions: 5 interactions with chain J, 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: J:Y.45, J:Y.45, J:K.58, J:K.58 Water bridges: J:Y.48 Hydrophobic interactions: A:L.110, A:A.114, A:L.145, C:M.31, C:F.35, C:F.35 DMU.48: 10 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.41 11 PLIP interactions: 4 interactions with chain J, 7 interactions with chain C Hydrophobic interactions: J:L.38, J:Y.45, J:Y.45, C:I.43 Hydrogen bonds: J:Y.45, C:N.36, C:N.36, C:N.36, C:S.37, C:S.37, C:S.37 DMU.65: 4 residues within 4Å: Chain C: W.32, M.38, L.41 Chain G: G.63 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:G.63 Hydrophobic interactions: C:W.32, C:W.32, C:L.41 DMU.74: 10 residues within 4Å: Chain A: L.35, F.459 Chain D: L.92, W.95 Chain M: L.27, L.28, G.31, W.32, Y.35, H.36 9 PLIP interactions: 3 interactions with chain D, 3 interactions with chain M, 3 interactions with chain A Hydrophobic interactions: D:L.92, D:W.95, M:L.27, M:L.27, A:L.35, A:F.459, A:F.459 Water bridges: D:Y.99, M:H.36

PEK.34: 9 residues within 4Å: Chain C: I.82, V.89, T.93, F.96, W.238, H.241, F.242, V.245, F.249 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.82, C:V.89, C:V.89, C:F.96, C:W.238, C:W.238, C:W.238, C:H.241, C:V.245 PEK.35: 27 residues within 4Å: Chain A: H.151, V.155, A.203, L.210, L.215 Chain C: W.32, F.33, Q.175, A.176, Y.179, Y.180, A.182, F.184, T.185, I.186, F.196, G.200, F.201, G.203, I.207 Chain G: W.62, T.68, F.69, F.70, H.71, N.76 Ligands: PGV.9 22 PLIP interactions: 4 interactions with chain A, 9 interactions with chain C, 9 interactions with chain G Hydrophobic interactions: A:V.155, A:A.203, A:L.210, A:L.215, C:W.32, C:F.33, C:Q.175, C:Y.179, C:I.186, C:F.201, C:F.201, C:I.207, G:W.62, G:F.69 Hydrogen bonds: C:I.186, G:T.68, G:F.70, G:F.70, G:N.76, G:N.76 Water bridges: G:F.69, G:F.69 PEK.36: 7 residues within 4Å: Chain C: Q.159, T.166, Y.170 Chain G: R.17, F.21, G.22, A.29 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: C:T.166, C:Y.170, C:Y.170, C:Y.170, G:F.21, G:A.29 Salt bridges: G:R.17 PEK.61: 1 residues within 4Å: Chain G: S.2 No protein-ligand interaction detected (PLIP)

CDL.39: 21 residues within 4Å: Chain C: M.49, L.50, Y.53, W.56, R.57, I.60, R.61, F.65, V.169, S.210, T.211, I.214, V.215, F.218, K.222, H.224 Chain J: K.8, F.12, T.27, L.31 Ligands: PGV.37 23 PLIP interactions: 3 interactions with chain J, 20 interactions with chain C Hydrophobic interactions: J:L.31, C:M.49, C:Y.53, C:Y.53, C:Y.53, C:W.56, C:W.56, C:R.57, C:V.169, C:T.211, C:I.214, C:V.215, C:F.218 Hydrogen bonds: J:D.28, C:Y.53 Salt bridges: J:K.8, C:R.61, C:K.222, C:K.222, C:H.224 Water bridges: C:R.57, C:R.57, C:R.61 CDL.62: 19 residues within 4Å: Chain C: N.123, L.125, L.129, T.132, S.133, L.136, V.140, L.248, Y.251, V.252, W.256 Chain G: L.23, S.27, L.30, C.31, L.33, N.34, H.38 Ligands: EDO.46 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain G