SMTL ID : 2ein.1

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized 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.34: 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: 3 residues within 4Å: Chain A: H.368, D.369 Chain B: E.198 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.368, A:D.369, B:E.198, H2O.164, H2O.165 MG.35: 3 residues within 4Å: Chain N: H.368, D.369 Chain O: E.198 5 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 2 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.569, H2O.713

NA.3: 4 residues within 4Å: Chain A: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.441 Water bridges: A:Q.43, A:D.442 NA.36: 4 residues within 4Å: Chain N: E.40, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:E.40 Water bridges: N:Q.43, N:D.442

HEA.4: 35 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, 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 29 PLIP interactions: 29 interactions with chain A, Hydrophobic interactions: A:I.37, A:A.62, A:M.65, A:I.66, A:V.374, 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 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:F.377, A:H.378 Metal complexes: A:H.61, A:H.378 HEA.5: 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, F.321, 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 39 PLIP interactions: 36 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:W.236, A:V.243, A:V.243, A:V.243, A:I.247, A:T.309, A:A.313, A:T.316, A:F.321, A:F.321, A:T.349, A:L.353, A:I.356, A:I.356, 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.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, A:R.439 Salt bridges: A:H.368, A:R.438 pi-Stacking: A:H.290 pi-Cation interactions: A:H.240, A:H.240, A:H.376 Metal complexes: A:H.376 HEA.39: 32 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, M.69, V.70, G.125, W.126, Y.371, V.374, F.377, H.378, L.381, S.382, V.386, T.424, F.425, Q.428, R.438, R.439, Y.440, S.458, V.465, M.468 31 PLIP interactions: 31 interactions with chain N, Hydrophobic interactions: N:T.31, N:V.58, N:A.62, N:M.65, N:V.70, N:V.374, N:F.377, N:L.381, N:V.386, N:V.386, N:T.424, N:F.425, N:F.425, N:V.465 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 Salt bridges: N:R.438, N:R.439 pi-Stacking: N:F.377, N:H.378, N:F.425 Metal complexes: N:H.61, N:H.378 HEA.40: 31 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, F.321, T.349, G.352, 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: 33 interactions with chain N, 4 interactions with chain O, Hydrophobic interactions: N:W.236, N:V.243, N:V.243, N:I.247, N:T.309, N:A.313, N:T.316, N:F.321, N:T.349, N:I.356, N:I.356, N:L.358, N:L.358, N:V.373, 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:I.72, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:H.291, N:H.291, N:T.316, N:D.369, N:D.369, N:R.438 Salt bridges: N:H.368, N:R.438 pi-Stacking: N:H.290 pi-Cation interactions: N:H.240 Metal complexes: N:H.376

TGL.6: 16 residues within 4Å: Chain A: Y.379, N.422, F.426, H.429, F.430, L.433, W.450 Chain B: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain I: R.43 15 PLIP interactions: 7 interactions with chain A, 1 interactions with chain I, 7 interactions with chain B Hydrophobic interactions: A:N.422, A:F.426, A:F.426, A:H.429, A:F.430, A:F.430, A:W.450, B:L.7, B:L.28, B:V.31, B:F.32, B:F.32 Salt bridges: I:R.43, B:H.24 Water bridges: B:L.7 TGL.7: 24 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain B: L.39, I.42, S.43, L.46, T.47, K.49 Chain D: R.73, S.74, T.75, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 17 PLIP interactions: 8 interactions with chain A, 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:K.411, A:F.414, A:F.414, A:F.418, D:W.78, D:V.81, D:V.81, D:I.89, B:L.39, B:I.42 Salt bridges: A:K.411 Hydrogen bonds: D:T.75, D:E.77, D:W.78 TGL.32: 27 residues within 4Å: Chain A: F.2, T.17, L.18, L.20, L.21, F.22, W.25, W.81, F.102, P.106, L.110, L.113, F.397, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, L.27, F.28, F.29, S.31, A.35 27 PLIP interactions: 9 interactions with chain L, 18 interactions with chain A Hydrophobic interactions: L:I.11, L:F.13, L:F.13, L:L.27, L:F.28, L:F.28, L:F.29, L:F.29, L:A.35, A:T.17, A:L.18, A:L.20, A:L.21, A:L.21, A:F.22, A:W.25, A:W.25, A:W.25, A:W.25, A:W.81, A:F.102, A:P.106, A:L.110, A:L.113, A:F.397, A:F.400, A:I.472 TGL.41: 23 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, K.411, F.414, A.415, F.418 Chain O: L.39, I.42, S.43, L.46, T.47, K.49 Chain Q: R.73, S.74, T.75, E.77, W.78, M.86, I.89 Chain V: R.16, H.20 16 PLIP interactions: 9 interactions with chain N, 4 interactions with chain Q, 3 interactions with chain O Hydrophobic interactions: N:W.334, N:W.334, N:L.342, N:K.411, N:F.414, N:A.415, N:F.418, N:F.418, Q:W.78, Q:I.89, O:L.39, O:I.42, O:L.46 Salt bridges: N:K.411 Hydrogen bonds: Q:E.77, Q:W.78 TGL.46: 17 residues within 4Å: Chain N: V.350, Y.379, N.422, F.426, P.427, H.429, F.430, L.433 Chain O: L.7, G.8, L.28, V.31, F.32, S.35, S.36, L.39 Chain V: R.43 15 PLIP interactions: 9 interactions with chain N, 5 interactions with chain O, 1 interactions with chain V Hydrophobic interactions: N:V.350, N:N.422, N:F.426, N:F.426, N:F.426, N:P.427, N:H.429, N:F.430, N:F.430, O:L.28, O:V.31, O:F.32, O:F.32 Salt bridges: O:H.24, V:R.43 TGL.63: 25 residues within 4Å: Chain N: T.17, L.18, L.20, L.21, F.22, W.25, W.81, L.110, L.113, F.393, F.397, F.400, S.401, I.472 Chain Y: I.11, P.12, F.13, S.14, R.20, M.24, L.27, F.28, F.29, S.31, A.35 24 PLIP interactions: 9 interactions with chain Y, 15 interactions with chain N Hydrophobic interactions: Y:I.11, Y:F.13, Y:F.13, Y:L.27, Y:F.28, Y:F.28, Y:F.29, Y:F.29, Y:A.35, N:T.17, N:L.18, N:L.20, N:L.21, N:L.21, N:W.25, N:W.25, N:W.25, N:W.25, N:W.81, N:L.113, N:F.393, N:F.397, N:F.400, N:I.472

PGV.8: 13 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: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 5 interactions with chain D, 2 interactions with chain K, 4 interactions with chain A, 4 interactions with chain M Hydrophobic interactions: D:T.80, D:F.87, D:F.87, D:F.87, D:F.87, K:F.9, A:T.408, A:W.409, A:W.409, M:P.12, M:A.16 Salt bridges: K:H.10 Hydrogen bonds: A:T.408 Water bridges: M:A.3, M:A.3 PGV.9: 29 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, F.148, H.151, 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, M.83, F.86, S.89, E.90, F.93 Ligands: PEK.17 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.24, C:T.28, C:T.53, C:W.57, C:W.57, C:W.57, C:W.58, C:F.86, C:F.93, A:F.148, A:V.155, A:V.155 Hydrogen bonds: C:W.57, A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.19: 28 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, M.83, F.86, E.90, F.93, H.207, I.209, I.210, T.213, F.214, R.221, H.226, F.227, T.228, H.231, H.232, F.233, G.234 Chain F: E.17 Ligands: PEK.17, CDL.21, ZN.25 28 PLIP interactions: 27 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:F.86, C:F.86, C:F.93, C:I.209, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, 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, F:Q.12 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 12 residues within 4Å: Chain A: D.298 Chain C: W.99, Y.102, H.103, L.106, A.107 Chain H: N.22, N.24 Chain P: W.258 Chain T: A.1 Ligands: CHD.16, CDL.61 6 PLIP interactions: 2 interactions with chain H, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: H:N.22 Water bridges: H:N.24, A:D.298, A:D.298 Hydrophobic interactions: C:W.99, C:W.99 PGV.42: 14 residues within 4Å: Chain N: N.406, T.408, W.409, I.412 Chain Q: T.80, A.84, F.87 Chain X: F.9, H.10 Chain Z: P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 3 interactions with chain X, 6 interactions with chain N, 3 interactions with chain Z, 3 interactions with chain Q Hydrophobic interactions: X:F.9, X:F.9, N:T.408, N:W.409, N:W.409, N:I.412, Z:P.12, Z:A.16, Z:L.19, Q:T.80, Q:F.87, Q:F.87 Salt bridges: X:H.10 Hydrogen bonds: N:N.406, N:T.408 PGV.43: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151, V.155 Chain P: H.9, G.20, A.24, M.27, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, E.90, F.93 Ligands: PEK.60 14 PLIP interactions: 8 interactions with chain N, 6 interactions with chain P