SMTL ID : 7d5x.1

Bovine heart cytochrome c oxidase in a catalytic intermediate, IO10, at 1.74 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, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: 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, 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: 34 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.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: OXY.7 36 PLIP interactions: 31 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:W.236, 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:F.348, A:L.353, A:I.356, A:I.356, A:L.358, A:V.373, A:F.377, A:F.377, A:V.380, A:V.380, 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.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376 HEA.86: 36 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, V.374, F.377, H.378, L.381, S.382, V.386, I.389, M.390, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, M.468 Ligands: TGL.92 37 PLIP interactions: 37 interactions with chain N, Hydrophobic interactions: N:R.38, N:V.58, N:V.58, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:F.377, N:F.377, N:L.381, N:L.381, N:V.386, N:V.386, N:I.389, N:F.393, N:F.393, N:T.424, N:F.425, 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.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.87: 33 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, 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: OXY.94 36 PLIP interactions: 31 interactions with chain N, 5 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:V.243, N:I.247, N:I.247, N:T.309, N:A.313, N:T.316, N:V.320, N:L.353, N:I.356, N:I.356, 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:T.316, N:D.369, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: OXY.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.88: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: OXY.94 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N: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.11, H2O.13, H2O.15 MG.89: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.65, H2O.67, H2O.67

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.40 NA.33: 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.90: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40 Water bridges: N:Q.43 NA.114: 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

PGV.6: 13 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.77, A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16, L.19, S.20 17 PLIP interactions: 6 interactions with chain D, 4 interactions with chain M, 2 interactions with chain K, 5 interactions with chain A Hydrophobic interactions: D:T.77, D:A.81, D:F.84, D:F.84, D:F.84, M:P.12, M:Q.15, M:A.16, M:L.19, K:F.4, A:T.408, A:W.409, A:W.409 Water bridges: D:E.74, K:H.5, A:T.408 Hydrogen bonds: A:T.408 PGV.8: 30 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, F.148, H.151, I.158, P.200 Chain C: H.7, V.9, G.18, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88 Ligands: PEK.35, PGV.37, DMU.51 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:F.148, A:I.158, A:P.200, C:A.22, C:T.51, C:W.55, C:W.55, C:W.55, C:W.56, C:F.84 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:W.55 Salt bridges: A:R.96 Water bridges: C:M.81 PGV.37: 25 residues within 4Å: Chain C: L.45, M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, M.81, F.84, E.88, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: PGV.8, CDL.39 27 PLIP interactions: 2 interactions with chain F, 25 interactions with chain C Water bridges: F:Q.12, F:E.17, C:S.63, C:R.219, C:H.229, C:H.229 Hydrophobic interactions: C:L.45, 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:I.208, C:I.208, C:F.212, C:F.212, C:F.212 Hydrogen bonds: C:S.63, C:R.219, C:F.231, C:G.232 Salt bridges: C:R.219, C:R.219, C:H.229 PGV.38: 9 residues within 4Å: Chain A: F.237, W.288 Chain C: T.93, W.97, Y.100, H.101, L.104 Ligands: CHD.32, CDL.145 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.237, A:W.288, C:T.93, C:W.97, C:W.97, C:W.97 Salt bridges: C:H.101 PGV.95: 30 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152 Chain P: H.7, V.9, G.18, A.22, M.25, T.26, N.48, T.51, M.52, W.55, W.56, V.59, E.62, H.69, L.77, G.80, F.84, S.87, E.88, F.91 Ligands: PEK.116, DMU.130 18 PLIP interactions: 11 interactions with chain P, 7 interactions with chain N Hydrophobic interactions: P:A.22, P:T.26, P:T.51, P:W.55, P:W.55, P:W.55, P:W.56, P:F.84, P:F.91, N:F.148, N:L.152 Hydrogen bonds: P:W.55, N:R.96, N:R.96, N:M.97 Water bridges: P:M.81, N:A.93 Salt bridges: N:R.96 PGV.118: 23 residues within 4Å: Chain P: M.49, M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, H.205, I.208, T.211, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 28 PLIP interactions: 2 interactions with chain S, 26 interactions with chain P Water bridges: S:Q.12, S:E.17, P:S.63, P:R.219, P:H.229, P:H.229 Hydrophobic interactions: P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:I.60, P:F.84, P:F.84, P:I.208, P:I.208, P:T.211, P:F.212, P:F.212, P:F.212 Hydrogen bonds: P:S.63, P:R.219, P:F.231, P:G.232 Salt bridges: P:R.219, P:R.219, P:H.229 PGV.119: 8 residues within 4Å: Chain G: A.1 Chain P: V.89, T.93, W.97, Y.100, H.101, L.104 Ligands: CHD.113 6 PLIP interactions: 5 interactions with chain P, 1 interactions with chain G Hydrophobic interactions: P:V.89, P:T.93, P:W.97, P:W.97, P:W.97, G:A.1 PGV.131: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: A.81, F.84 Chain X: F.4, H.5 Chain Z: P.12, Q.15, A.16, L.19, S.20 13 PLIP interactions: 2 interactions with chain X, 4 interactions with chain Z, 3 interactions with chain N, 4 interactions with chain Q Hydrophobic interactions: X:F.4, X:F.4, Z:P.12, Z:P.12, Z:A.16, Z:L.19, N:W.409, N:W.409, Q:F.84, Q:F.84, Q:F.84, Q:F.84 Hydrogen bonds: N:T.408

OXY.7: 6 residues within 4Å: Chain A: H.240, V.243, H.290, H.291 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) OXY.94: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.87, CU.88 No protein-ligand interaction detected (PLIP)

EDO.9: 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.10: 7 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain M: I.1 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: E.119, A.120 Chain L: Q.42, K.45, K.46 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: G.269, Y.270, M.271, G.272 Chain B: A.58, Q.59, E.62 Ligand excluded by PLIP EDO.13: