SMTL ID : 7cp5.1

Bovine heart cytochrome c oxidase in a catalytic intermediate of E at 1.76 angstrom resolution

HEA.1: 36 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, I.389, F.393, M.417, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 Ligands: TGL.77 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:I.37, A:R.38, 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:L.381, A:L.381, A:V.386, A:V.386, A:I.389, 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:H.378, 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: PER.8 40 PLIP interactions: 34 interactions with chain A, 5 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: 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.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, 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, A:H.240, A:H.376 Metal complexes: A:H.376, H2O.1 HEA.81: 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.91 29 PLIP interactions: 29 interactions with chain N, Hydrophobic interactions: N:A.24, N:I.37, N:R.38, N:A.62, N:M.65, N:I.66, N:V.70, N:L.381, N:L.381, N:F.393, N:F.393, N:T.424 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.82: 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.89 39 PLIP interactions: 33 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:V.243, N:I.247, N:I.247, N:T.309, N:T.316, 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: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, N:H.240, N:H.376 Metal complexes: N:H.376, H2O.62

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: PER.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.7 CU.83: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: PER.89 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.69

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.13, H2O.15 MG.84: 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.70, H2O.74, H2O.74

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:S.441 Water bridges: A:Q.43 NA.27: 3 residues within 4Å: Chain C: H.146, H.230, E.234 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.234, C:E.234 NA.85: 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:Q.43 Water bridges: N:Q.43 NA.108: 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: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: A.81, F.84 Chain K: F.4, H.5 Chain M: P.12, Q.15, A.16, L.19 13 PLIP interactions: 3 interactions with chain M, 6 interactions with chain A, 2 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: M:P.12, M:Q.15, M:L.19, A:T.408, A:W.409, A:W.409, A:W.409, D:A.81, D:F.84, K:F.4, K:F.4 Hydrogen bonds: A:T.408 Water bridges: A:T.408 PGV.26: 30 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158, 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, F.84, S.87, F.91 Ligands: PEK.32 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:F.148, A:L.152, A:I.158, A:L.159, 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.84, C:F.84, C:F.91 Hydrogen bonds: A:R.96, A:M.97, C:W.55 Salt bridges: A:R.96 PGV.33: 22 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, H.205, I.208, F.212, R.219, H.224, F.225, T.226, H.229, H.230, F.231, G.232 Ligands: CDL.30 26 PLIP interactions: 24 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: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 Water bridges: C:S.63, 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.36: 6 residues within 4Å: Chain A: F.237 Chain C: T.93, W.97, Y.100, H.101 Ligands: CHD.29 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:T.93, C:W.97, C:W.97, C:W.97, A:F.237 Salt bridges: C:H.101 PGV.62: 5 residues within 4Å: Chain G: A.1 Chain P: T.93, W.97, H.101 Ligands: CHD.107 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain P Hydrophobic interactions: G:A.1, P:T.93, P:W.97, P:W.97 Salt bridges: P:H.101 PGV.86: 13 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: T.77, A.81, F.84 Chain X: F.4, H.5 Chain Z: P.12, Q.15, A.16, L.19 11 PLIP interactions: 3 interactions with chain N, 4 interactions with chain Z, 2 interactions with chain Q, 2 interactions with chain X Hydrophobic interactions: N:T.408, N:W.409, N:I.412, Z:P.12, Z:P.12, Z:Q.15, Z:L.19, Q:T.77, Q:F.84, X:F.4, X:F.4 PGV.87: 29 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, L.152, I.158 Chain P: 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, M.81, F.84, S.87, F.91 Ligands: PEK.112 18 PLIP interactions: 10 interactions with chain P, 8 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, N:I.158 Hydrogen bonds: P:W.55, N:R.96, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.113: 25 residues within 4Å: Chain P: M.52, W.56, V.59, I.60, S.63, T.64, H.69, L.77, M.81, F.84, E.88, F.91, 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.110 25 PLIP interactions: 23 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.56, P:W.56, P:W.56, P:W.56, P:W.56, P:I.60, P:F.84, P:F.91, P:I.208, P:T.211, P:F.212, P:F.212 Hydrogen bonds: P:S.63, P:R.219, P:F.231, P:G.232 Water bridges: P:S.63, P:R.219, P:H.229, P:H.229, S:Q.12, S:E.17 Salt bridges: P:R.219, P:R.219, P:H.229

PSC.7: 14 residues within 4Å: Chain A: F.321, A.325, H.328 Chain B: I.41, M.45, H.52, M.56, D.57, V.61, I.64, W.65, L.68, P.69 Chain I: L.17 12 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:I.41, B:I.41, B:M.56, B:I.64, B:W.65, B:W.65, B:W.65, B:L.68, B:P.69, A:F.321, A:A.325, I:L.17 PSC.103: 15 residues within 4Å: Chain N: F.321, A.325, H.328 Chain O: I.41, M.45, H.52, M.56, D.57, E.60, V.61, I.64, W.65, L.68, P.69 Ligands: DMU.102 13 PLIP interactions: 10 interactions with chain O, 3 interactions with chain N Hydrophobic interactions: O:I.41, O:I.41, O:M.56, O:W.65, O:W.65, O:L.68, O:P.69, N:F.321, N:F.321, N:A.325 Hydrogen bonds: O:D.57 Water bridges: O:T.55 Salt bridges: O:H.52

PER.8: 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) PER.89: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.82,