SMTL ID : 7d5w.1

Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution

HEA.1: 35 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, V.374, 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.82 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:F.393, A:T.424, A:F.425 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.425 Metal complexes: A:H.61, A:H.378 HEA.2: 35 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, F.321, F.348, 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: PER.9 38 PLIP interactions: 5 interactions with chain B, 32 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: B:I.34, B:I.34, B:P.69, B:I.72, B:L.73, A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:I.247, A:T.309, A:T.316, A:V.320, A:F.321, A:F.348, A:T.349, A:I.356, A:I.356, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381, A:L.381 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 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376, H2O.1 HEA.90: 34 residues within 4Å: Chain N: 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.96 32 PLIP interactions: 32 interactions with chain N, Hydrophobic interactions: N:I.37, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:F.377, N:L.381, N:L.381, N:V.386, N:V.386, N:F.393, N:F.393, N:T.424, N:F.425 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, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.425 Metal complexes: N:H.61, N:H.378 HEA.91: 34 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, V.320, F.348, 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 O: I.34, P.69, I.72, L.73 Ligands: PER.99 37 PLIP interactions: 31 interactions with chain N, 5 interactions with chain O, 1 Ligand-Water interactions, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:V.320, N:F.348, N:I.356, N:I.356, N:L.358, 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:P.69, O:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:H.291, N:T.316, N:D.369, N:D.369, N:R.438, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376, H2O.64

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.9 CU.92: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: PER.99 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.71

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.12, H2O.12, H2O.16 MG.93: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 3 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.71, H2O.74, H2O.76

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 NA.31: 3 residues within 4Å: Chain C: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.230 NA.94: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:Q.43 NA.118: 3 residues within 4Å: Chain P: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:E.234

TGL.6: 18 residues within 4Å: Chain A: F.346, V.350, Y.379, N.422, F.426, P.427, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, L.28, F.32, S.35, S.36, L.39 Chain I: R.43 20 PLIP interactions: 6 interactions with chain B, 12 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: B:F.32, B:F.32, B:L.39, A:F.346, A:V.350, A:N.422, A:F.426, A:F.426, A:F.426, A:F.426, A:F.426, A:P.427, A:F.430, A:L.433, A:W.450 Water bridges: B:G.8, B:F.9, I:R.43 Salt bridges: B:H.24, I:R.43 TGL.7: 26 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, V.419 Chain B: L.39, I.42, L.46, T.47, T.48, K.49 Chain D: R.70, S.71, T.72, E.74, W.75, V.78, M.83, I.86 Chain I: R.16, H.20 Ligands: DMU.23, DMU.57 14 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, B:L.46, B:K.49, A:W.334, A:W.334, A:V.419, D:W.75, D:V.78, D:V.78, D:I.86 Hydrogen bonds: D:T.72, D:E.74, D:W.75 TGL.82: 25 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, F.102, P.106, F.109, L.113, F.393, F.400, S.401 Chain L: N.9, I.10, P.11, F.12, S.13, R.19, M.23, M.24, F.27, F.28, S.30 Ligands: HEA.1 18 PLIP interactions: 7 interactions with chain L, 11 interactions with chain A Hydrophobic interactions: L:I.10, L:F.12, L:F.12, L:F.12, L:F.27, L:F.28, L:F.28, A:T.17, A:L.18, A:L.21, A:F.22, A:F.22, A:W.25, A:W.25, A:F.102, A:F.109, A:L.113, A:F.393 TGL.95: 20 residues within 4Å: Chain N: F.346, T.354, Y.379, F.418, V.419, N.422, M.423, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35 Chain V: K.42, R.43 14 PLIP interactions: 1 interactions with chain V, 4 interactions with chain O, 9 interactions with chain N Salt bridges: V:R.43, O:H.24 Hydrophobic interactions: O:V.31, O:F.32, N:T.354, N:F.418, N:M.423, N:F.426, N:F.426, N:F.426, N:F.426, N:H.429, N:F.430 Water bridges: O:G.8 TGL.96: 26 residues within 4Å: Chain N: T.17, L.18, L.20, L.21, W.25, W.81, P.106, F.109, L.110, L.112, L.113, F.393, F.400, S.401, I.472 Chain Y: N.9, I.10, P.11, F.12, S.13, R.19, M.23, F.27, F.28, S.30 Ligands: HEA.90 21 PLIP interactions: 12 interactions with chain N, 9 interactions with chain Y Hydrophobic interactions: N:T.17, N:L.18, N:L.20, N:W.25, N:W.25, N:W.81, N:F.109, N:F.109, N:L.112, N:L.113, N:I.472, N:I.472, Y:I.10, Y:F.12, Y:F.12, Y:F.27, Y:F.27, Y:F.27, Y:F.27, Y:F.28, Y:F.28 TGL.97: 16 residues within 4Å: Chain N: W.334, L.342, F.414, A.415, V.419 Chain O: L.39, I.42, L.46, T.47 Chain Q: R.70, S.71, E.74, W.75, V.78, M.83, I.86 12 PLIP interactions: 7 interactions with chain N, 3 interactions with chain O, 2 interactions with chain Q Hydrophobic interactions: N:W.334, N:W.334, N:W.334, N:L.342, N:F.414, N:A.415, N:V.419, O:L.39, O:L.46, O:T.47, Q:W.75, Q:I.86

PGV.8: 14 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, A.16, L.19, S.20 Ligands: DMU.79 14 PLIP interactions: 6 interactions with chain M, 5 interactions with chain A, 1 interactions with chain K, 2 interactions with chain D Hydrophobic interactions: M:P.12, M:Q.15, M:A.16, M:L.19, A:W.409, A:W.409, A:W.409, A:I.412, K:F.4, D:A.81, D:F.84 Water bridges: M:A.3, M:A.3 Hydrogen bonds: A:T.408 PGV.11: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, L.159, 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, S.87, F.91 Ligands: PEK.33, PGV.35 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.22, C:T.26, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.91, A:F.148, A:L.152, A:L.159, A:P.200 Hydrogen bonds: C:W.55, A:R.96, A:R.96, A:M.97 Salt bridges: A:R.96 PGV.35: 24 residues within 4Å: Chain C: M.49, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, E.88, F.91, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.11, CDL.37 29 PLIP interactions: 27 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:W.56, C:I.60, C:F.84, C:F.91, C:I.208, C:I.208, C:I.208, C:F.212, C:F.212, C:F.212, C:F.212