SMTL ID : 7thu.1

Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays

CU.1: 3 residues within 4Å: Chain A: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.240, A:H.290, A:H.291 CU.83: 3 residues within 4Å: Chain N: H.240, H.290, H.291 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:H.240, N:H.290, N:H.291

MG.2: 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.9, H2O.9, H2O.12 MG.84: 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.37, H2O.38, H2O.39

NA.3: 4 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40, A:E.40 Water bridges: A:Q.43 NA.85: 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:E.40

PGV.4: 11 residues within 4Å: Chain A: N.406, T.408, W.409 Chain D: T.80, A.84, F.87 Chain K: F.9, H.10 Chain M: T.10, P.12, Q.15 9 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: A:T.408, A:W.409, A:W.409, D:F.87, D:F.87, K:F.9, K:F.9 Hydrogen bonds: A:N.406, A:W.409 PGV.5: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, H.151, L.152, V.155 Chain C: H.9, V.11, G.20, A.24, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90 Ligands: PEK.32, PGV.34 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C Hydrophobic interactions: A:L.152, A:V.155, C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86 Hydrogen bonds: A:R.96, A:R.96, A:M.97, C:E.64 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.34: 25 residues within 4Å: Chain C: M.51, M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Ligands: PGV.5, DMU.30, CDL.35 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:S.65, C:R.221, C:H.231, C:H.231, F:Q.12, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.87: 24 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, L.152 Chain P: H.9, V.11, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, S.89, E.90, F.93 Ligands: PEK.110 12 PLIP interactions: 5 interactions with chain N, 7 interactions with chain P Hydrophobic interactions: N:L.152, P:A.24, P:T.28, P:W.57, P:W.57, P:W.57, P:W.58, P:F.93 Hydrogen bonds: N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.98: 9 residues within 4Å: Chain G: A.1 Chain N: W.288, D.298 Chain P: T.95, W.99, Y.102, H.103, A.107 Ligands: CHD.109 11 PLIP interactions: 3 interactions with chain N, 6 interactions with chain P, 1 interactions with chain G, 1 interactions with chain O Hydrophobic interactions: N:W.288, P:T.95, P:W.99, P:W.99, P:W.99, P:Y.102, G:A.1 Hydrogen bonds: N:D.298 Water bridges: N:D.298, O:R.178 Salt bridges: P:H.103 PGV.112: 20 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, F.86, H.207, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 28 PLIP interactions: 26 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:I.210, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:T.66, P:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:H.231, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.131: 15 residues within 4Å: Chain A: W.288, G.296, M.297, D.298, Y.304 Chain B: R.178 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain T: A.1, S.2 Ligands: CHD.31, CDL.132 11 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C, 5 interactions with chain A, 1 interactions with chain T Hydrogen bonds: B:R.178, A:D.298, A:D.298 Hydrophobic interactions: C:T.95, C:W.99, C:W.99, C:W.99, A:W.288, A:Y.304, T:A.1 Water bridges: A:T.301 PGV.148: 22 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, E.474, S.478, R.480 Chain Q: T.80, A.84, F.87, F.88 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.5, A.6, T.10, P.12, Q.15, A.16 Ligands: EDO.149 14 PLIP interactions: 3 interactions with chain Q, 6 interactions with chain N, 4 interactions with chain Z, 1 interactions with chain X Hydrophobic interactions: Q:A.84, Q:F.87, Q:F.88, N:T.408, N:W.409, N:I.412, Z:P.12, Z:A.16, X:F.9 Water bridges: N:T.404, N:T.404, Z:A.6 Salt bridges: N:R.480 Hydrogen bonds: Z:A.3

HEA.6: 31 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, L.73 35 PLIP interactions: 31 interactions with chain A, 4 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:L.358, 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:L.73 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:D.369, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376 HEA.7: 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, V.374, F.377, H.378, L.381, S.382, V.386, F.393, M.417, V.421, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 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:V.374, A:F.377, A:F.377, A:L.381, A:L.381, A:F.393, A:V.421, A:T.424, A:F.425, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, 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 Salt bridges: A:R.438, A:R.439 Metal complexes: A:H.61, A:H.378 HEA.88: 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.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 O: I.34, P.69, I.72, L.73 35 PLIP interactions: 30 interactions with chain N, 5 interactions with chain O, Hydrophobic interactions: N:W.236, 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.321, 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, O:I.34, O:I.34, O:P.69, O:I.72, O:L.73 Hydrogen bonds: N:Y.244, N:Y.244, N:D.364 Water bridges: N:D.369, N:D.369, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 Metal complexes: N:H.376 HEA.89: 35 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, F.425, Q.428, R.438, R.439, Y.440, S.461, V.465, M.468 33 PLIP interactions: 33 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, 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:F.393, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:Y.54, N:Y.54, N:W.126, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:H.61 Metal complexes: N:H.61, N:H.378

EDO.8: 8 residues within 4Å: Chain A: L.483, T.484, V.485, W.494, G.497, C.498 Chain D: Y.11 Ligands: EDO.13 Ligand excluded by PLIP EDO.9: 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.10: 6 residues within 4Å: Chain A: H.256, T.259, K.265, T.490, N.491 Ligands: EDO.62 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: W.334, S.335, P.336, D.407, K.411 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Q.52, A.120, A.137, H.138, A.139 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: V.482, L.483, G.497, C.498 Chain D: S.8, Y.11 Ligands: EDO.8 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: E.266, P.267, G.269, Y.270 Chain F: S.67 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: G.269, M.271, G.272 Chain B: A.58, E.62 Ligands: CHD.22 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: K.265, T.489 Chain F: I.70, P.83, S.84 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, H.94 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: K.265, E.266 Chain B: T.55 Chain F: N.66, T.68, I.70, S.84 Ligand excluded by PLIP EDO.20: 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.23: 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.24: 4 residues within 4Å: Chain A: L.136, A.137 Chain B: D.158, V.159 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: M.146, E.147, P.215, L.216 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: H.22, F.23, H.26, P.79, R.82 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: S.94, L.95, Y.113, M.148, F.219 Chain H: Q.12 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: K.217, Y.218, K.221 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: N.92, P.93 Chain H: Q.12, T.13, A.14, P.15 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain C: W.146, S.150, H.158 Chain F: A.1 Chain G: A.13, R.14, R.17 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain C: H.243, V.247 Ligands: EDO.39 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain C: H.243 Ligands: EDO.38, PEK.44, DMU.64 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain C: I.45, T.48 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain C: N.12, P.13 Chain J: G.17, L.18, P.19 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain D: W.48, S.49, L.51, S.52, I.53, K.56 Ligands: EDO.56 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain D: P.25, D.26, V.27, A.28, K.63 Chain E: R.30 Ligand excluded by PLIP EDO.48: