SMTL ID : 6juw.1

BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION

HEA.1: 36 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, V.70, I.73, G.125, W.126, Y.371, 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 32 PLIP interactions: 32 interactions with chain A, Hydrophobic interactions: A:A.24, A:I.37, A:V.58, A:V.58, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:L.381, A:L.381, A:V.386, A:V.386, A:F.393, A:T.424, A:F.425 Hydrogen bonds: A:R.38, A:Y.54, A:W.126, A:Y.371, 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, 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 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: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: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.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Cation interactions: A:H.290 Metal complexes: A:H.376, H2O.1 HEA.83: 37 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, I.66, M.69, V.70, I.73, 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 32 PLIP interactions: 32 interactions with chain N, Hydrophobic interactions: N:A.24, N:I.37, 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:L.381, N:L.381, 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.84: 32 residues within 4Å: Chain N: W.126, W.236, V.243, Y.244, I.247, H.290, H.291, T.309, 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 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:A.313, N:T.316, N:V.320, N:F.348, N:L.353, 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 Metal complexes: N:H.376, H2O.54

CU.3: 3 residues within 4Å: Chain A: H.240, H.290, H.291 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.4 CU.85: 3 residues within 4Å: Chain N: H.240, H.290, H.291 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.59

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, A:D.369, H2O.8, H2O.11, H2O.13 MG.86: 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.64, H2O.65, 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:S.441 NA.27: 3 residues within 4Å: Chain C: H.146, H.230, E.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.146 NA.87: 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:D.442 Water bridges: N:Q.43 NA.110: 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

DMU.6: 5 residues within 4Å: Chain A: M.423 Chain D: I.86 Chain K: V.21, W.24, V.25 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:V.21, K:W.24, K:W.24, K:W.24, K:V.25, D:I.86 DMU.21: 7 residues within 4Å: Chain B: H.26, I.30, L.33, I.34, L.37, I.72, L.75 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.30, B:L.33, B:I.34, B:L.37, B:I.72, B:L.75 Hydrogen bonds: B:H.26 DMU.28: 9 residues within 4Å: Chain C: N.36, S.37, T.39, I.43 Chain J: L.38, G.41, G.42, Y.45 Ligands: DMU.69 8 PLIP interactions: 4 interactions with chain J, 4 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:S.37 DMU.29: 5 residues within 4Å: Chain C: W.32, M.38, L.41 Chain G: F.69 Ligands: PGV.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:W.32, C:L.41 Water bridges: G:F.69 DMU.30: 4 residues within 4Å: Chain C: Y.100, F.249, V.252 Ligands: CDL.65 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.249, C:F.249, C:F.249, C:V.252 DMU.44: 6 residues within 4Å: Chain D: L.91, I.94, W.95, H.98 Chain K: Y.26, I.31 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.95 Salt bridges: D:H.98 DMU.69: 12 residues within 4Å: Chain A: L.110, L.145 Chain C: S.27, T.30, M.31, F.35 Chain J: S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.28 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A, 1 interactions with chain J Hydrophobic interactions: C:T.30, C:F.35, C:F.35, A:L.110, A:L.145 Hydrogen bonds: J:Y.45 DMU.72: 4 residues within 4Å: Chain K: V.25, A.28, W.35 Ligands: DMU.75 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:V.25, K:A.28, K:W.35 DMU.73: 4 residues within 4Å: Chain K: A.28, I.33, W.35 Ligands: DMU.75 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:W.35, K:W.35, K:W.35 Hydrogen bonds: K:T.29, K:I.33 DMU.74: 6 residues within 4Å: Chain D: F.84 Chain K: A.14, S.15, T.18, F.19 Ligands: PGV.7 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain D Hydrophobic interactions: K:F.19, D:F.84 Hydrogen bonds: K:S.15, K:T.18 DMU.75: 3 residues within 4Å: Ligands: TGL.45, DMU.72, DMU.73 No protein-ligand interaction detected (PLIP) DMU.76: 10 residues within 4Å: Chain A: M.117 Chain J: F.55 Chain L: S.30, A.34, F.37, R.40, H.41, L.44 Ligands: TGL.78, EDO.80 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:A.34 Hydrogen bonds: L:R.40, L:H.41 Water bridges: L:R.40, L:R.40 Salt bridges: L:R.40, L:R.40 DMU.81: 12 residues within 4Å: Chain A: F.459 Chain D: L.92, W.95, Y.99 Chain M: L.27, L.28, A.30, G.31, W.32, L.34, Y.35, H.36 7 PLIP interactions: 3 interactions with chain M, 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: M:L.27, M:A.30, A:F.459, D:L.92, D:W.95, D:W.95 Water bridges: M:Y.35 DMU.107: 7 residues within 4Å: Chain O: H.26, M.29, I.30, L.33, L.37, I.72, L.75 5 PLIP interactions: 5 interactions with chain O Hydrophobic interactions: O:L.33, O:L.37, O:I.72, O:L.75 Hydrogen bonds: O:H.26 DMU.111: 3 residues within 4Å: Chain P: W.32, M.38 Chain T: F.69 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain T Hydrophobic interactions: P:W.32, P:W.32, T:F.69 DMU.112: 11 residues within 4Å: Chain P: M.31, N.36, S.37, T.39, I.43 Chain W: T.37, L.38, G.41, G.42, Y.45 Ligands: DMU.147 7 PLIP interactions: 3 interactions with chain P, 4 interactions with chain W Hydrogen bonds: P:N.36, P:S.37, P:S.37 Hydrophobic interactions: W:L.38, W:Y.45, W:Y.45, W:Y.45 DMU.127: 8 residues within 4Å: Chain Q: L.91, I.94, W.95, H.98 Chain X: Y.26, Q.30, I.31, G.32 4 PLIP interactions: 1 interactions with chain X, 3 interactions with chain Q Hydrogen bonds: X:Y.26 Hydrophobic interactions: Q:L.91, Q:I.94 Salt bridges: Q:H.98 DMU.147: 13 residues within 4Å: Chain N: L.110, A.114, L.145 Chain P: S.27, M.31, F.35 Chain W: Y.45, S.46, Y.48, C.49, L.50, W.52 Ligands: DMU.112 8 PLIP interactions: