Copper in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb 3ag4)

The binding sites of Copper atom in the structure of Bovine Heart Cytochrome C Oxidase in the Cyanide Ion-Bound Fully Reduced State At 100 K (pdb code 3ag4). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3ag4 structure was solved by K.MURAMOTO, K.OHTA, K.SHINZAWA-ITOH, K.KANDA, M.TANIGUCHI, H.NABEKURA, E.YAMASHITA, T.TSUKIHARA, S.YOSHIKAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.0 Space group P212121 a (A) 183.364 b (A) 206.648 c (A) 178.137 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 21.9 Copper Binding Sites: Copper binding site 1 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3ag4. 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: Trp236, A: His240, A: Val243, A: His290, A: His291, A: Hea516, A: Cyn520, A: Hoh4310, conact list: Atom Atom Distance (A) Cu CZ3 A:Trp236 5.00 Cu O A:His240 4.93 Cu NE2 A:His240 4.03 Cu N A:His240 4.68 Cu CB A:His240 3.40 Cu ND1 A:His240 1.97 Cu CD2 A:His240 4.12 Cu C A:His240 4.87 Cu CE1 A:His240 2.90 Cu CG A:His240 3.03 Cu CA A:His240 3.85 Cu CG2 A:Val243 4.36 Cu NE2 A:His290 2.78 Cu ND1 A:His290 4.80 Cu CD2 A:His290 3.72 Cu CE1 A:His290 3.68 Cu CG A:His290 4.86 Cu NE2 A:His291 2.03 Cu ND1 A:His291 4.14 Cu CD2 A:His291 3.03 Cu CE1 A:His291 3.03 Cu CG A:His291 4.16 Cu NA A:Hea516 4.93 Cu ND A:Hea516 4.87 Cu FE A:Hea516 4.99 Cu C1A A:Hea516 4.93 Cu N A:Cyn520 2.26 Cu C A:Cyn520 2.88 Cu O A:Hoh4310 4.75 interactive model: Copper binding site 2 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3ag4. 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: His102, B: Trp104, B: Trp106, B: Leu160, B: His161, B: Cys196, B: Glu198, B: Cys200, B: His204, B: Met207, B: Cua228, conact list: Atom Atom Distance (A) Cu O B:His102 4.65 Cu CD1 B:Trp104 4.49 Cu CZ2 B:Trp106 4.99 Cu O B:Leu160 4.76 Cu NE2 B:His161 4.05 Cu CB B:His161 3.57 Cu ND1 B:His161 1.99 Cu CD2 B:His161 4.18 Cu CE1 B:His161 2.86 Cu CG B:His161 3.12 Cu CA B:His161 4.18 Cu CB B:Cys196 3.47 Cu SG B:Cys196 2.38 Cu CA B:Cys196 4.86 Cu O B:Glu198 4.05 Cu CB B:Cys200 3.33 Cu SG B:Cys200 2.37 Cu CA B:Cys200 4.78 Cu O B:His204 4.98 Cu ND1 B:His204 4.48 Cu CA B:His204 4.68 Cu CB B:Met207 4.82 Cu CE B:Met207 2.98 Cu CG B:Met207 3.49 Cu SD B:Met207 2.35 Cu CU1 B:Cua228 0.00 Cu CU2 B:Cua228 2.53 interactive model: Copper binding site 3 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3ag4. 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: Ser197, B: Glu198, B: Ile199, B: Cys200, B: His204, B: Met207, B: Cua228, conact list: Atom Atom Distance (A) Cu CB B:His161 4.98 Cu ND1 B:His161 4.11 Cu CE1 B:His161 4.97 Cu CG B:His161 4.97 Cu CA B:His161 4.81 Cu O B:Cys196 4.25 Cu CB B:Cys196 3.33 Cu SG B:Cys196 2.28 Cu C B:Cys196 4.18 Cu CA B:Cys196 4.39 Cu N B:Ser197 4.60 Cu O B:Glu198 2.34 Cu N B:Glu198 4.25 Cu C B:Glu198 3.56 Cu CA B:Glu198 4.60 Cu N B:Ile199 4.36 Cu C B:Ile199 4.29 Cu CA B:Ile199 4.28 Cu N B:Cys200 3.71 Cu CB B:Cys200 3.48 Cu SG B:Cys200 2.30 Cu CA B:Cys200 4.26 Cu O B:His204 3.76 Cu NE2 B:His204 4.03 Cu N B:His204 4.68 Cu CB B:His204 3.64 Cu ND1 B:His204 2.01 Cu CD2 B:His204 4.19 Cu C B:His204 4.10 Cu CE1 B:His204 2.85 Cu CG B:His204 3.16 Cu CA B:His204 3.48 Cu CG B:Met207 4.68 Cu SD B:Met207 4.38 Cu CU1 B:Cua228 2.53 Cu CU2 B:Cua228 0.00 interactive model: Copper binding site 4 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3ag4. 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: Val243, N: Val287, N: His290, N: His291, N: Hea516, N: Cyn520, N: Hoh4406, conact list: Atom Atom Distance (A) Cu O N:His240 4.94 Cu NE2 N:His240 4.08 Cu N N:His240 4.62 Cu CB N:His240 3.29 Cu ND1 N:His240 1.98 Cu CD2 N:His240 4.13 Cu C N:His240 4.88 Cu CE1 N:His240 2.95 Cu CG N:His240 2.99 Cu CA N:His240 3.78 Cu CG2 N:Val243 4.39 Cu CG1 N:Val243 4.76 Cu CG2 N:Val287 4.89 Cu NE2 N:His290 2.64 Cu ND1 N:His290 4.67 Cu CD2 N:His290 3.67 Cu CE1 N:His290 3.50 Cu CG N:His290 4.79 Cu NE2 N:His291 1.99 Cu ND1 N:His291 4.05 Cu CD2 N:His291 3.05 Cu CE1 N:His291 2.90 Cu CG N:His291 4.14 Cu NA N:Hea516 4.93 Cu ND N:Hea516 5.00 Cu C1A N:Hea516 4.97 Cu N N:Cyn520 2.44 Cu C N:Cyn520 2.98 Cu O N:Hoh4406 4.83 interactive model: Copper binding site 5 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3ag4. 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: His102, O: Trp104, O: Leu160, O: His161, O: Cys196, O: Glu198, O: Cys200, O: His204, O: Met207, O: Cua228, conact list: Atom Atom Distance (A) Cu O O:His102 4.68 Cu CD1 O:Trp104 4.34 Cu O O:Leu160 4.75 Cu NE2 O:His161 3.99 Cu CB O:His161 3.59 Cu ND1 O:His161 1.99 Cu CD2 O:His161 4.16 Cu CE1 O:His161 2.79 Cu CG O:His161 3.13 Cu CA O:His161 4.27 Cu CB O:Cys196 3.43 Cu SG O:Cys196 2.30 Cu CA O:Cys196 4.81 Cu O O:Glu198 4.00 Cu CB O:Cys200 3.33 Cu SG O:Cys200 2.39 Cu CA O:Cys200 4.74 Cu ND1 O:His204 4.60 Cu CA O:His204 4.78 Cu CB O:Met207 4.87 Cu CE O:Met207 3.00 Cu CG O:Met207 3.52 Cu SD O:Met207 2.40 Cu CU1 O:Cua228 0.00 Cu CU2 O:Cua228 2.63 interactive model: Copper binding site 6 out of 6 in 3ag4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3ag4. 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: Ser197, O: Glu198, O: Ile199, O: Cys200, O: His204, O: Met207, O: Cua228, conact list: Atom Atom Distance (A) Cu CB O:His161 4.99 Cu ND1 O:His161 4.11 Cu CE1 O:His161 4.95 Cu CA O:His161 4.91 Cu O O:Cys196 4.22 Cu CB O:Cys196 3.27 Cu SG O:Cys196 2.28 Cu C O:Cys196 4.24 Cu CA O:Cys196 4.39 Cu N O:Ser197 4.73 Cu O O:Glu198 2.24 Cu N O:Glu198 4.22 Cu C O:Glu198 3.43 Cu CA O:Glu198 4.43 Cu N O:Ile199 4.27 Cu C O:Ile199 4.29 Cu CA O:Ile199 4.27 Cu N O:Cys200 3.65 Cu CB O:Cys200 3.36 Cu SG O:Cys200 2.28 Cu CA O:Cys200 4.11 Cu O O:His204 3.87 Cu NE2 O:His204 4.09 Cu N O:His204 4.69 Cu CB O:His204 3.46 Cu ND1 O:His204 2.02 Cu CD2 O:His204 4.17 Cu C O:His204 4.15 Cu CE1 O:His204 2.95 Cu CG O:His204 3.07 Cu CA O:His204 3.51 Cu CG O:Met207 4.75 Cu SD O:Met207 4.44 Cu CU1 O:Cua228 2.63 Cu CU2 O:Cua228 0.00 interactive model: