Copper in the structure of Structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb 1occ)

The binding sites of Copper atom in the structure of Structure of Bovine Heart Cytochrome C Oxidase At the Fully Oxidized State (pdb code 1occ). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1occ structure was solved by T.TSUKIHARA, H.AOYAMA, E.YAMASHITA, T.TOMIZAKI, H.YAMAGUCHI, K.SHINZAWA-ITOH, R.NAKASHIMA, R.YAONO, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.8 Space group P212121 a (A) 189.100 b (A) 210.500 c (A) 178.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.1 Rfree (%) 25.2 Copper Binding Sites: Copper binding site 1 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His240, A: His290, A: His291, A: Hea516, conact list: Atom Atom Distance (A) Cu NE2 A:His240 3.85 Cu CB A:His240 3.64 Cu ND1 A:His240 1.85 Cu CD2 A:His240 4.06 Cu CE1 A:His240 2.64 Cu CG A:His240 3.05 Cu CA A:His240 4.20 Cu NE2 A:His290 2.16 Cu ND1 A:His290 4.25 Cu CD2 A:His290 3.19 Cu CE1 A:His290 3.09 Cu CG A:His290 4.32 Cu NE2 A:His291 2.15 Cu ND1 A:His291 4.22 Cu CD2 A:His291 2.99 Cu CE1 A:His291 3.17 Cu CG A:His291 4.15 Cu NA A:Hea516 4.40 Cu CHA A:Hea516 4.88 Cu C2A A:Hea516 4.86 Cu C4A A:Hea516 4.67 Cu C3A A:Hea516 4.87 Cu FE A:Hea516 4.70 Cu C1A A:Hea516 4.54 interactive model: Copper binding site 2 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Trp104, B: Leu160, B: His161, B: Cys196, B: Glu198, B: Cys200, B: His204, B: Met207, B: Cu229, conact list: Atom Atom Distance (A) Cu CD1 B:Trp104 4.99 Cu O B:Leu160 4.65 Cu NE2 B:His161 3.87 Cu CB B:His161 3.68 Cu ND1 B:His161 1.89 Cu CD2 B:His161 4.09 Cu CE1 B:His161 2.63 Cu CG B:His161 3.09 Cu CA B:His161 4.10 Cu CB B:Cys196 3.48 Cu SG B:Cys196 2.27 Cu CA B:Cys196 4.84 Cu O B:Glu198 3.83 Cu N B:Cys200 4.89 Cu CB B:Cys200 3.32 Cu SG B:Cys200 2.30 Cu CA B:Cys200 4.69 Cu O B:His204 4.83 Cu ND1 B:His204 4.25 Cu CA B:His204 4.95 Cu CE B:Met207 3.22 Cu CG B:Met207 3.68 Cu SD B:Met207 2.48 Cu CU B:Cu229 2.38 interactive model: Copper binding site 3 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His161, B: Cys196, B: Glu198, B: Ile199, B: Cys200, B: His204, B: Met207, B: Cu228, conact list: Atom Atom Distance (A) Cu ND1 B:His161 4.05 Cu CE1 B:His161 4.65 Cu O B:Cys196 4.52 Cu CB B:Cys196 3.43 Cu SG B:Cys196 2.26 Cu C B:Cys196 4.64 Cu CA B:Cys196 4.66 Cu O B:Glu198 2.18 Cu N B:Glu198 4.32 Cu C B:Glu198 3.42 Cu CA B:Glu198 4.43 Cu O B:Ile199 4.92 Cu N B:Ile199 4.27 Cu C B:Ile199 4.12 Cu CA B:Ile199 4.26 Cu N B:Cys200 3.56 Cu CB B:Cys200 3.33 Cu SG B:Cys200 2.21 Cu C B:Cys200 4.92 Cu CA B:Cys200 4.07 Cu O B:His204 3.61 Cu NE2 B:His204 3.94 Cu N B:His204 4.86 Cu CB B:His204 3.54 Cu ND1 B:His204 1.92 Cu CD2 B:His204 4.06 Cu C B:His204 4.03 Cu CE1 B:His204 2.76 Cu CG B:His204 3.02 Cu CA B:His204 3.58 Cu CG B:Met207 4.53 Cu SD B:Met207 4.12 Cu CU B:Cu228 2.38 interactive model: Copper binding site 4 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: N: His240, N: His290, N: His291, N: Hea516, conact list: Atom Atom Distance (A) Cu NE2 N:His240 3.85 Cu CB N:His240 3.64 Cu ND1 N:His240 1.85 Cu CD2 N:His240 4.06 Cu CE1 N:His240 2.64 Cu CG N:His240 3.05 Cu CA N:His240 4.20 Cu NE2 N:His290 2.16 Cu ND1 N:His290 4.25 Cu CD2 N:His290 3.19 Cu CE1 N:His290 3.09 Cu CG N:His290 4.32 Cu NE2 N:His291 2.15 Cu ND1 N:His291 4.22 Cu CD2 N:His291 2.99 Cu CE1 N:His291 3.17 Cu CG N:His291 4.15 Cu NA N:Hea516 4.40 Cu CHA N:Hea516 4.88 Cu C2A N:Hea516 4.86 Cu C4A N:Hea516 4.67 Cu C3A N:Hea516 4.87 Cu FE N:Hea516 4.70 Cu C1A N:Hea516 4.54 interactive model: Copper binding site 5 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: Trp104, O: Leu160, O: His161, O: Cys196, O: Glu198, O: Cys200, O: His204, O: Met207, O: Cu229, conact list: Atom Atom Distance (A) Cu CD1 O:Trp104 4.99 Cu O O:Leu160 4.65 Cu NE2 O:His161 3.87 Cu CB O:His161 3.68 Cu ND1 O:His161 1.89 Cu CD2 O:His161 4.09 Cu CE1 O:His161 2.63 Cu CG O:His161 3.09 Cu CA O:His161 4.10 Cu CB O:Cys196 3.48 Cu SG O:Cys196 2.27 Cu CA O:Cys196 4.84 Cu O O:Glu198 3.84 Cu N O:Cys200 4.89 Cu CB O:Cys200 3.32 Cu SG O:Cys200 2.30 Cu CA O:Cys200 4.69 Cu O O:His204 4.83 Cu ND1 O:His204 4.25 Cu CA O:His204 4.95 Cu CE O:Met207 3.22 Cu CG O:Met207 3.68 Cu SD O:Met207 2.48 Cu CU O:Cu229 2.38 interactive model: Copper binding site 6 out of 6 in 1occ Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1occ. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: His161, O: Cys196, O: Glu198, O: Ile199, O: Cys200, O: His204, O: Met207, O: Cu228, conact list: Atom Atom Distance (A) Cu ND1 O:His161 4.05 Cu CE1 O:His161 4.65 Cu O O:Cys196 4.52 Cu CB O:Cys196 3.43 Cu SG O:Cys196 2.26 Cu C O:Cys196 4.64 Cu CA O:Cys196 4.66 Cu O O:Glu198 2.18 Cu N O:Glu198 4.32 Cu C O:Glu198 3.42 Cu CA O:Glu198 4.43 Cu O O:Ile199 4.92 Cu N O:Ile199 4.27 Cu C O:Ile199 4.12 Cu CA O:Ile199 4.26 Cu N O:Cys200 3.56 Cu CB O:Cys200 3.34 Cu SG O:Cys200 2.21 Cu C O:Cys200 4.92 Cu CA O:Cys200 4.06 Cu O O:His204 3.61 Cu NE2 O:His204 3.94 Cu N O:His204 4.86 Cu CB O:His204 3.53 Cu ND1 O:His204 1.92 Cu CD2 O:His204 4.06 Cu C O:His204 4.03 Cu CE1 O:His204 2.76 Cu CG O:His204 3.02 Cu CA O:His204 3.58 Cu CG O:Met207 4.53 Cu SD O:Met207 4.12 Cu CU O:Cu228 2.38 interactive model: