SMTL ID : 7tii.1

Annealed structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure

HEA.1: 36 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, S.382, V.386, M.390, F.393, M.417, T.424, 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:T.31, 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:V.374, A:F.377, A:F.377, A:F.393, 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:Q.428, A:R.439, A:Y.440 Water bridges: A:S.461 Salt bridges: A:R.438, A:R.439 pi-Stacking: A:H.61, 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, 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 Ligands: OH.10 37 PLIP interactions: 33 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.236, A:V.243, A:I.247, A:I.247, A:T.309, A:T.316, A:V.320, A:F.348, A:T.349, A:I.356, A:I.356, A:L.358, A:L.358, A:V.373, A:V.373, A:F.377, A:F.377, A:V.380, A:V.380, A:L.381, A:L.381, A:L.381, B:I.34, B:I.72, B:L.73 Hydrogen bonds: A:W.126, A:Y.244, A:Y.244 Water bridges: A:D.369, A:D.369, A:R.439 Salt bridges: A:H.368, A:R.438, A:R.439 pi-Stacking: A:H.290 Metal complexes: A:H.376, OH.10 HEA.33: 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, S.382, V.386, M.390, F.393, V.421, T.424, F.425, Q.428, R.438, R.439, Y.440, V.465, M.468 36 PLIP interactions: 36 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:I.73, N:V.374, N:F.377, N:V.386, N:V.386, N:F.393, N:V.421, 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 Metal complexes: N:H.61, N:H.378 HEA.34: 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, 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 Ligands: OH.40 35 PLIP interactions: 29 interactions with chain N, 5 interactions with chain O, 1 Ligand-Ligand interactions Hydrophobic interactions: 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: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:T.316, N:D.369, N:R.438 Salt bridges: N:H.368, N:R.438, N:R.439 pi-Cation interactions: N:H.240, N:H.290 Metal complexes: N:H.376, OH.40

CU.3: 4 residues within 4Å: Chain A: H.240, H.290, H.291 Ligands: OH.10 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.240, A:H.290, A:H.291, H2O.1, OH.10 CU.35: 4 residues within 4Å: Chain N: H.240, H.290, H.291 Ligands: OH.40 5 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: N:H.240, N:H.290, N:H.291, H2O.21, OH.40

MG.4: 4 residues within 4Å: Chain A: H.368, D.369 Chain B: S.197, E.198 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.198, A:H.368, H2O.6, H2O.7, H2O.7 MG.36: 4 residues within 4Å: Chain N: H.368, D.369 Chain O: S.197, E.198 6 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N, 3 Ligand-Water interactions Metal complexes: O:E.198, N:H.368, N:D.369, H2O.25, H2O.25, H2O.26

NA.5: 5 residues within 4Å: Chain A: E.40, G.45, T.46, S.441, D.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.40 NA.37: 5 residues within 4Å: Chain N: E.40, G.45, T.46, S.441, D.442 2 PLIP interactions: 2 interactions with chain N Hydrogen bonds: N:E.40, N:G.45

PGV.6: 24 residues within 4Å: Chain A: F.94, P.95, R.96, M.97, M.100, V.155 Chain C: H.9, V.11, G.20, T.28, N.50, T.53, W.57, W.58, V.61, E.64, H.71, V.75, L.79, F.86, S.89, E.90 Ligands: PEK.14, PGV.15 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:V.155, 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:M.97, C:H.9, C:W.57 Salt bridges: A:R.96 Water bridges: C:M.83 PGV.7: 17 residues within 4Å: Chain A: N.406, T.408, W.409, R.480 Chain D: T.80, A.84, F.87, F.88 Chain K: F.9, H.10 Chain M: K.4, P.5, P.12, Q.15, A.16, L.19, S.20 15 PLIP interactions: 5 interactions with chain D, 3 interactions with chain K, 5 interactions with chain A, 2 interactions with chain M Hydrophobic interactions: D:T.80, D:A.84, D:F.87, D:F.87, D:F.88, K:F.9, K:F.9, A:T.408, A:W.409, A:W.409, A:W.409, M:P.12, M:L.19 Salt bridges: K:H.10 Hydrogen bonds: A:T.408 PGV.15: 23 residues within 4Å: Chain C: M.51, W.58, V.61, I.62, 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 Ligands: PGV.6, CDL.16 25 PLIP interactions: 1 interactions with chain F, 24 interactions with chain C Water bridges: F:E.17, C:R.221, C:H.231 Hydrophobic interactions: 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:I.210, C:T.213, C:F.214, C:F.214 Hydrogen bonds: C:S.65, C:H.71, C:R.221, C:F.233, C:G.234 Salt bridges: C:R.221, C:R.221, C:H.231 PGV.20: 10 residues within 4Å: Chain A: F.237, D.298 Chain C: W.99, Y.102, H.103, L.106 Chain H: N.22, N.24 Ligands: CHD.18, CDL.57 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: A:F.237, C:W.99, C:W.99 Salt bridges: C:H.103 Hydrogen bonds: H:N.22 PGV.43: 25 residues within 4Å: Chain N: F.94, P.95, R.96, M.97, M.100 Chain P: H.9, G.20, S.23, A.24, L.31, N.50, M.54, W.57, W.58, V.61, E.64, H.71, L.79, G.82, M.83, F.86, E.90, F.93 Ligands: PGV.45, PEK.54 15 PLIP interactions: 4 interactions with chain N, 11 interactions with chain P Hydrogen bonds: N:R.96, N:M.97, P:H.9, P:W.57, P:E.64 Water bridges: N:A.93 Salt bridges: N:R.96 Hydrophobic interactions: P:A.24, P:L.31, P:W.57, P:W.57, P:W.57, P:W.58, P:F.86, P:F.93 PGV.44: 12 residues within 4Å: Chain C: W.258 Chain G: A.1 Chain N: F.237, D.298 Chain P: V.91, W.99, H.103, A.107 Chain U: N.22, N.24 Ligands: CDL.26, CHD.48 10 PLIP interactions: 4 interactions with chain U, 1 interactions with chain C, 4 interactions with chain P, 1 interactions with chain N Hydrogen bonds: U:N.22, U:N.24 Water bridges: U:N.22, U:N.24 Hydrophobic interactions: C:W.258, P:V.91, P:W.99, P:W.99, N:F.237 Salt bridges: P:H.103 PGV.45: 24 residues within 4Å: Chain P: M.51, M.54, W.58, V.61, I.62, 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 Ligands: PGV.43, CDL.46 26 PLIP interactions: 25 interactions with chain P, 1 interactions with chain S Hydrophobic interactions: P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:W.58, P:I.62, P:F.86, P:I.210, P:I.210, P:I.210, P:T.213, P:F.214, P:F.214, P:F.214 Hydrogen bonds: P:S.65, P:R.221, P:F.233, P:G.234 Water bridges: P:R.221, P:H.231, P:H.231, S:E.17 Salt bridges: P:R.221, P:R.221, P:H.231 PGV.63: 15 residues within 4Å: Chain N: N.406, T.408, W.409, I.412, R.480 Chain Q: A.84 Chain X: F.9, H.10 Chain Z: A.3, K.4, P.5, P.12, Q.15, A.16, S.20 12 PLIP interactions: 5 interactions with chain N, 4 interactions with chain Z, 1 interactions with chain Q, 2 interactions with chain X Hydrophobic interactions: N:W.409, N:W.409, N:I.412, Z:P.12, Z:P.12, Q:A.84, X:F.9 Hydrogen bonds: N:T.408 Water bridges: N:T.404, Z:A.3, Z:A.6 Salt bridges: X:H.10

EDO.8: 6 residues within 4Å: Chain A: Y.260, Y.261, V.394, H.395, P.398, W.494 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.260, A:Y.261, A:H.395 EDO.9: 6 residues within 4Å: Chain A: E.507 Chain C: T.5 Chain F: P.30, N.32, P.50, R.56 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: C:T.5, A:E.507, F:N.32 EDO.21: 8 residues within 4Å: Chain C: W.146, S.150, D.155, H.158 Chain F: A.1 Chain G: A.13, R.14, R.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:S.150, F:A.1 EDO.29: 5 residues within 4Å: Chain C: G.120 Chain G: A.46, F.47, I.48, R.54 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:A.46, G:I.48, G:R.54, G:R.54, C:G.120 EDO.39: 7 residues within 4Å: Chain N: Y.260, Y.261, V.394, H.395, P.398, W.494 Chain Z: I.1 3 PLIP interactions: 3 interactions with chain N Hydrogen bonds: N:Y.260, N:V.394, N:H.395 EDO.51: 7 residues within 4Å: Chain N: E.507 Chain P: T.5 Chain S: P.30, N.32, P.50, R.56, L.96 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain S Hydrogen bonds: N:E.507, S:P.30, S:N.32 EDO.52: 7 residues within 4Å: Chain P: W.146, S.150, H.158 Chain S: A.1 Chain T: A.13, R.14, R.17 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain S Hydrogen bonds: P:W.146, S:A.1 EDO.58: 8 residues within 4Å: Chain P: G.120 Chain T: P.45, A.46, F.47, I.48, L.53, R.54, Y.82 4 PLIP interactions: 3 interactions with chain T, 1 interactions with chain P Hydrogen bonds: T:I.48, T:R.54, T:R.54, P:G.120

OH.10: 5 residues within 4Å: Chain A: H.240, V.243, H.290 Ligands: HEA.2, CU.3 No protein-ligand interaction detected (PLIP) OH.40: 4 residues within 4Å: Chain N: H.240, H.290 Ligands: HEA.34, CU.35 No protein-ligand interaction detected (PLIP)

TGL.11: 15 residues within 4Å: Chain A: F.346, Y.379, N.422, F.426, F.430, L.433, W.450 Chain B: L.7, G.8, H.24, L.28, V.31, F.32, S.35 Chain I: R.43 10 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: B:V.31, A:F.346, A:F.426, A:F.426, A:F.430, A:L.433, A:W.450 Hydrogen bonds: B:G.8 Water bridges: B:F.9 Salt bridges: I:R.43 TGL.22: 18 residues within 4Å: Chain A: W.334, M.339, L.342, G.343, K.411, F.414, A.415 Chain B: I.42, S.43, T.47, K.49 Chain D: R.73, T.75, E.77, W.78, V.81 Chain I: R.16, H.20 10 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:W.334, A:W.334, A:L.342, A:F.414, A:A.415, B:I.42, D:W.78, D:V.81 Salt bridges: A:K.411 Hydrogen bonds: D:W.78 TGL.32: 20 residues within 4Å: Chain A: F.2, T.17, L.18, L.21, F.22, W.25, W.81, F.393, F.397, F.400, I.472 Chain L: I.11, P.12, F.13, S.14, R.20, M.24, M.25, F.28, F.29 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain L Hydrophobic interactions: A:F.2, A:L.18, A:F.22, A:W.25, A:W.81, A:F.393, A:F.397, A:F.400,