SMTL ID : 2eim.1

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

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.29: 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 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, H2O.188, H2O.189, H2O.190 MG.30: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 5 PLIP interactions: 2 interactions with chain N, 1 interactions with chain O, 2 Ligand-Water interactions Metal complexes: N:H.368, N:D.369, O:E.198, H2O.837, H2O.838

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 Water bridges: A:Q.43, A:G.45 NA.31: 5 residues within 4Å: Chain N: E.40, Q.43, G.45, T.46, S.441 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:Q.43 Water bridges: N:Q.43, N:G.45

ZN.4: 2 residues within 4Å: Chain A: H.503 Chain L: H.2 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: A:H.503, L:H.2, H2O.54, H2O.55 ZN.14: 3 residues within 4Å: Chain C: H.148, H.232, E.236 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.148, C:H.232, C:E.236, H2O.279 ZN.23: 4 residues within 4Å: Chain F: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.82, F:C.85 ZN.32: 2 residues within 4Å: Chain N: H.503 Chain Y: H.2 4 PLIP interactions: 1 interactions with chain N, 1 interactions with chain Y, 2 Ligand-Water interactions Metal complexes: N:H.503, Y:H.2, H2O.1203, H2O.1204 ZN.43: 3 residues within 4Å: Chain P: H.148, H.232, E.236 5 PLIP interactions: 4 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.148, P:H.232, P:E.236, P:E.236, H2O.912 ZN.51: 4 residues within 4Å: Chain S: C.60, C.62, C.82, C.85 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.60, S:C.62, S:C.82, S:C.85

HEA.5: 32 residues within 4Å: Chain A: A.24, 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.417, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:I.37, A:A.62, A:M.65, A:I.66, A:V.70, A:I.73, A:V.374, A:F.377, A:F.377, A:L.381, A:L.381, 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, A:R.438, A:S.461, A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, A:F.425 Metal complexes: A:H.61, A:H.378 HEA.6: 32 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, I.72, L.73 33 PLIP interactions: 5 interactions with chain B, 28 interactions with chain A, Hydrophobic interactions: B:I.34, B:I.34, B:P.69, B:I.72, B:L.73, A:W.236, A:V.243, A:Y.244, A:I.247, A:I.247, A:T.309, A:A.313, A:T.316, A:V.320, A:T.349, A:I.356, A:I.356, A:V.373, A:F.377, A:F.377, A:V.380, A:L.381 Hydrogen bonds: A:W.126, A:Y.244 Water bridges: A:T.316, A:H.368, A:D.369, A:R.438, A:R.439 Salt bridges: A:H.368, A:R.438 pi-Cation interactions: A:H.240 Metal complexes: A:H.376 HEA.33: 31 residues within 4Å: Chain N: A.24, M.28, 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.425, Q.428, R.438, R.439, Y.440, V.465, M.468 33 PLIP interactions: 33 interactions with chain N, Hydrophobic interactions: N:I.37, N:A.62, N:M.65, N:I.66, N:V.70, N:V.374, N:L.381, N:V.386, N:F.425, N:F.425, N:F.425, N:V.465, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:Y.54, N:W.126, N:Y.371, N:Q.428, N:R.439, N:Y.440 Water bridges: N:R.438, N:R.438, N:S.461, N:S.461 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:H.61, N:F.377, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.34: 32 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 37 PLIP interactions: 5 interactions with chain O, 32 interactions with chain N, Hydrophobic interactions: O:I.34, O:I.34, O:P.69, O:I.72, O:L.73, N:W.236, N:V.243, N:V.243, N:V.243, N:Y.244, 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 Hydrogen bonds: N:Y.244 Water bridges: N:T.316, N:H.368, N:D.369, N:R.438, 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

PGV.7: 13 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: A.84, F.87 Chain K: F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 14 PLIP interactions: 4 interactions with chain D, 5 interactions with chain A, 4 interactions with chain M, 1 interactions with chain K Hydrophobic interactions: D:A.84, D:F.87, D:F.87, D:F.87, A:T.408, A:W.409, A:W.409, A:I.412, M:P.12, M:A.16, M:L.19 Hydrogen bonds: A:T.408 Water bridges: M:A.3 Salt bridges: K:H.10 PGV.17: 26 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, V.155 Chain C: H.9, V.11, G.20, M.27, T.28, N.50, T.53, M.54, W.57, W.58, E.64, H.71, L.79, G.82, S.89, E.90, F.93 Ligands: PEK.15, PGV.18 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:F.148, A:V.155, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.93 Hydrogen bonds: A:R.96, A:M.97, C:W.57 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.18: 24 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, F.86, E.90, 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: PEK.15, PGV.17, CDL.20 29 PLIP interactions: 28 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:F.86, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214, C:F.233 Hydrogen bonds: C:S.65, C:R.221, C:F.233, C:G.234 Water bridges: C:R.221, C:H.231, C:H.231, F:E.17 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.19: 12 residues within 4Å: Chain A: F.237 Chain C: T.95, W.99, Y.102, H.103, A.107 Chain H: N.22, N.24 Chain P: W.258 Chain T: A.1 Ligands: CHD.8, CDL.53 9 PLIP interactions: 3 interactions with chain A, 2 interactions with chain H, 3 interactions with chain C, 1 interactions with chain P Hydrophobic interactions: A:F.237, C:T.95, C:W.99, C:W.99, P:W.258 Water bridges: A:D.298, A:D.298 Hydrogen bonds: H:N.22, H:N.24 PGV.38: 12 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: A.84, F.87 Chain X: H.10 Chain Z: P.12, Q.15, A.16, L.19, S.20 13 PLIP interactions: 3 interactions with chain Z, 1 interactions with chain X, 5 interactions with chain Q, 4 interactions with chain N Hydrophobic interactions: Z:P.12, Z:A.16, Z:L.19, Q:A.84, Q:F.87, Q:F.87, Q:F.87, Q:F.87, N:T.408, N:W.409, N:I.412 Salt bridges: X:H.10 Hydrogen bonds: N:T.408 PGV.47: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, V.155 Chain P: H.9, V.11, G.20, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, S.89, E.90, F.93 Ligands: PEK.45, PGV.48 12 PLIP interactions: 7 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:T.28, P:W.57, P:W.57, P:W.57, P:F.86, P:F.93, N:F.148 Hydrogen bonds: P:W.57, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.48: 25 residues within 4Å: Chain P: M.54, W.58, V.61, I.62, S.65, T.66, H.71, L.79, M.83, E.90, 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: PEK.45, PGV.47, CDL.50 25 PLIP interactions: 22 interactions with chain P, 3 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:I.62, P:I.210, P:I.210, P:I.210, P:F.214, P:F.214, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:F.233, P:G.234 Water bridges: P:R.221, P:H.231, S:Q.12, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.49: 10 residues within 4Å: Chain C: W.258 Chain N: F.237 Chain P: T.95, W.99, Y.102, H.103, A.107 Chain U: N.24 Ligands: CDL.24, CHD.44 5 PLIP interactions: 2 interactions with chain P, 2 interactions with chain U, 1 interactions with chain N Hydrophobic interactions: P:T.95, P:W.99, N:F.237 Hydrogen bonds: U:N.22 Water bridges: U:N.24

CHD.8: 8 residues within 4Å: Chain A: H.233, D.300, T.301, Y.304 Chain C: W.99, H.103 Ligands: PGV.19, CDL.53 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.304, A:Y.304 Hydrogen bonds: A:D.300, A:D.300, A:T.301, C:W.99 Salt bridges: A:H.233, C:H.103 CHD.12: 12 residues within 4Å: Chain A: M.271, W.275 Chain B: Q.59, E.62, T.63, T.66 Chain T: R.14, R.17, F.18, F.21, G.22 Ligands: PEK.46 13 PLIP interactions: 4 interactions with chain A, 5 interactions with chain T, 4 interactions with chain B Hydrophobic interactions: A:M.271, A:W.275, A:W.275, A:W.275, T:F.18, T:F.18, B:E.62, B:T.66 Hydrogen bonds: T:R.17, B:E.62, B:T.63 Water bridges: T:R.17 Salt bridges: T:R.14 CHD.21: 7 residues within 4Å: Chain C: R.156, K.157, L.160, Q.161, F.164, L.223 Chain J: F.1 8 PLIP interactions: 1 interactions with chain J, 7 interactions with chain C Hydrogen bonds: J:F.1, C:Q.161 Hydrophobic interactions: C:K.157, C:L.160, C:F.164, C:F.164, C:L.223 Salt bridges: C:R.156 CHD.26: 5 residues within 4Å: Chain J: Y.32, R.33, M.36, T.37, L.40 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:Y.32, J:R.33, J:M.36, J:L.40 Hydrogen bonds: J:R.33 CHD.35: 13 residues within 4Å: Chain G: R.14, R.17, F.18, F.21, G.22 Chain N: M.271, G.272, W.275 Chain O: Q.59, E.62, T.63, T.66 Ligands: PEK.16 14 PLIP interactions: 4 interactions with chain N, 3 interactions with chain O, 7 interactions with chain G Hydrophobic interactions: N:M.271, N:W.275, N:W.275, N:W.275, O:E.62, G:F.18, G:F.21