SMTL ID : 5wau.1

Crystal Structure of CO-bound Cytochrome c Oxidase determined by Synchrotron X-Ray Crystallography at 100 K

HEA.1: 37 residues within 4Å: Chain A: L.20, 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, T.424, F.425, Q.428, R.438, R.439, Y.440, S.461, V.465, M.468 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:A.24, 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:L.381, A:L.381, A:F.393, A:T.424, A:F.425, A:F.425, A:V.465 Hydrogen bonds: A:S.34, A:S.34, A:R.38, A:W.126, 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:F.377, A:F.425 pi-Cation interactions: A:H.378 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, L.73 Ligands: CMO.10 37 PLIP interactions: 33 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:W.236, 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:F.377, A:F.377, A:V.380, A:L.381, 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, A:Y.244, A:H.290 Water bridges: A:H.368, A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 Metal complexes: A:H.376 HEA.29: 38 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, S.461, V.465, M.468 39 PLIP interactions: 39 interactions with chain N, Hydrophobic interactions: N:A.24, N:T.31, N:R.38, 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.393, N:T.424, N:F.425, N:F.425, N:F.425, N:V.465 Hydrogen bonds: N:S.34, N:S.34, N:R.38, N:W.126, N:Y.371, 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:F.425 pi-Cation interactions: N:H.378 Metal complexes: N:H.61, N:H.378 HEA.30: 33 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, L.73 Ligands: CMO.36 35 PLIP interactions: 32 interactions with chain N, 3 interactions with chain O, 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: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, N:L.381, O:I.34, O:P.69, O:L.73 Hydrogen bonds: N:W.126, N:Y.244 Water bridges: N:H.291, N:T.316, N:D.369, N:R.438, N:R.439 Salt bridges: N:H.368, N:R.438, N:R.439 Metal complexes: N:H.376

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: CMO.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, CMO.10 CU.31: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: CMO.36 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, CMO.36

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.11, H2O.11, H2O.14 MG.32: 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.53, H2O.54

NA.5: 5 residues within 4Å: Chain A: E.40, Q.43, G.45, S.441, D.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.45 Water bridges: A:Q.43, A:T.46 NA.33: 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, N:S.441, N:D.442

PGV.6: 15 residues within 4Å: Chain A: N.406, T.408, W.409, I.412 Chain D: A.84, F.87, F.91 Chain K: D.8, F.9, H.10 Chain M: P.12, Q.15, A.16, L.19, S.20 12 PLIP interactions: 4 interactions with chain A, 3 interactions with chain M, 1 interactions with chain K, 4 interactions with chain D Hydrophobic interactions: A:T.408, A:W.409, A:W.409, A:I.412, M:Q.15, M:A.16, M:L.19, K:F.9, D:A.84, D:F.87, D:F.87, D:F.91 PGV.7: 28 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, L.104, L.152, I.158, L.159 Chain C: H.9, V.11, G.20, A.24, M.27, T.28, N.50, T.53, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, F.86, E.90 Ligands: PEK.14 18 PLIP interactions: 9 interactions with chain C, 9 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, A:L.104, A:L.152, A:I.158, A:L.159 Hydrogen bonds: C:H.9, A:R.96, A:R.96, A:M.97 Water bridges: A:A.93 Salt bridges: A:R.96 PGV.15: 22 residues within 4Å: Chain C: M.54, W.58, V.61, I.62, S.65, T.66, H.71, 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: PEK.14, CDL.17 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: C:W.58, C:W.58, C:W.58, C:W.58, C:I.62, C:I.210, C:I.210, C:I.210, C:T.213, C:F.214, C:F.214, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:T.66, C:H.71, 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.16: 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, W.259 Chain T: A.1 Ligands: CHD.13 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain C Hydrogen bonds: H:N.22, H:N.24 Water bridges: H:N.22 Hydrophobic interactions: C:W.99, C:W.99, C:L.106, C:L.106 PGV.34: 16 residues within 4Å: Chain N: N.406, T.408, W.409 Chain Q: T.80, A.84, F.91 Chain X: F.9, H.10, S.20 Chain Z: P.9, T.10, S.11, P.12, Q.15, L.19, S.20 7 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain N, 4 interactions with chain Z Hydrophobic interactions: Q:A.84, Q:F.91, N:W.409, Z:P.12, Z:L.19 Hydrogen bonds: Z:T.10 Water bridges: Z:A.6 PGV.35: 26 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100, F.148, H.151 Chain P: H.9, G.20, A.24, T.28, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, S.89, E.90 Ligands: PEK.43, PGV.45 13 PLIP interactions: 8 interactions with chain P, 5 interactions with chain N Hydrophobic interactions: P:A.24, P:T.28, P:W.57, P:W.57, P:W.57, P:W.58, N:F.148 Hydrogen bonds: P:H.9, P:E.64, N:R.96, N:M.97 Water bridges: N:A.93 Salt bridges: N:R.96 PGV.41: 11 residues within 4Å: Chain C: W.258, W.259 Chain G: A.1 Chain N: D.298 Chain P: T.95, W.99, H.103, L.106, A.107 Chain U: N.24 Ligands: CHD.42 6 PLIP interactions: 4 interactions with chain P, 1 interactions with chain N, 1 interactions with chain U Hydrophobic interactions: P:W.99, P:W.99, P:L.106 Hydrogen bonds: P:H.103, N:D.298 Water bridges: U:N.24 PGV.45: 25 residues within 4Å: Chain P: M.54, W.58, V.61, S.65, T.66, H.71, L.79, M.83, F.86, E.90, L.206, 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.35, CDL.46 29 PLIP interactions: 27 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:F.86, P:F.86, P:L.206, 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:H.71, P:R.221, P:F.233, P:G.234 Water bridges: P:S.65, P:R.221, P:T.228, P:H.231, S:Q.12, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231

TGL.8: 15 residues within 4Å: Chain A: V.350, N.422, F.426, H.429, F.430, L.433 Chain B: M.5, L.7, G.8, L.28, V.31, F.32, S.35, L.39 Chain I: R.43 12 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: A:V.350, A:N.422, A:F.426, A:H.429, A:F.430, A:F.430, A:L.433, B:L.7, B:V.31, B:F.32, B:L.39 Salt bridges: I:R.43 TGL.9: 22 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.103, P.106, L.113, F.393, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29, S.31 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain L Hydrophobic interactions: A:F.2, A:L.18, A:F.22, A:W.25, A:W.25, A:W.103, A:L.113, A:F.393, A:F.400, A:I.472, L:I.11, L:F.13, L:F.13, L:F.13, L:F.28, L:F.28, L:F.28, L:F.29 TGL.21: 20 residues within 4Å: Chain A: W.334, M.339, L.342, K.411, F.414, A.415 Chain B: L.39, I.42, L.46, T.47, T.48, K.49 Chain D: R.73, E.77, W.78, V.81, M.86, I.89 Chain I: R.16, H.20 13 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: B:L.39, B:I.42, B:K.49, A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, D:V.81, D:I.89 Salt bridges: A:K.411 Water bridges: D:T.75, D:E.77 TGL.38: 13 residues within 4Å: Chain N: N.422, F.426, H.429, F.430, L.433 Chain O: L.7, G.8, H.24, L.28, V.31, F.32, S.35 Chain V: R.43 8 PLIP interactions: 3 interactions with chain N, 4 interactions with chain O, 1 interactions with chain V Hydrophobic interactions: N:H.429, N:F.430, N:L.433, O:L.28, O:V.31, O:F.32 Water bridges: O:F.9 Salt bridges: V:R.43 TGL.49: 18 residues within 4Å: Chain N: W.334, M.339, L.342, G.343, F.414, A.415 Chain O: L.39, I.42, S.43, T.47 Chain Q: R.73, S.74, T.75, E.77, W.78, V.81, M.86 Chain V: R.16 11 PLIP interactions: 4 interactions with chain N, 5 interactions with chain Q, 2 interactions with chain O Hydrophobic interactions: N:W.334, N:L.342, N:F.414, N:A.415, Q:E.77, Q:W.78, Q:V.81, O:L.39, O:I.42 Hydrogen bonds: Q:E.77, Q:W.78 TGL.53: 22 residues within 4Å: Chain N: F.2, L.7, T.17, L.18, L.20, L.21, F.22, W.25, L.113, F.393, F.400, I.472 Chain Y: I.11, P.12, F.13, S.14, M.24, M.25, L.27, F.28, F.29, A.35 22 PLIP interactions: 12 interactions with chain N, 10 interactions with chain Y Hydrophobic interactions: N:F.2, N:T.17, N:L.18, N:L.20, N:W.25, N:W.25, N:W.25, N:W.25, N:L.113, N:F.393, N:F.400, N:I.472, Y:I.11, Y:F.13, Y:F.13, Y:L.27, Y:F.28, Y:F.28, Y:F.28, Y:F.29, Y:F.29, Y:A.35

CMO.10: 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) CMO.36: 6 residues within 4Å: Chain N: H.240, V.243, H.290, H.291 Ligands: HEA.30, CU.31 No protein-ligand interaction detected (PLIP)

CUA.11: 6 residues within 4Å: Chain B: H.161, C.196, E.198, C.200, H.204, M.207 7 PLIP interactions: 7 interactions with chain B