Copper in the structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State At 100 K (pdb 3ag3)

The binding sites of Copper atom in the structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State At 100 K (pdb code 3ag3). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3ag3 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) 40.0-1.8 Space group P212121 a (A) 182.289 b (A) 208.358 c (A) 177.916 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 20.3 Copper Binding Sites: Copper binding site 1 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3ag3. 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: Val243, A: Val287, A: Trp288, A: His290, A: His291, A: Hea516, A: No520, conact list: Atom Atom Distance (A) Cu NE2 A:His240 4.15 Cu N A:His240 4.78 Cu CB A:His240 3.30 Cu ND1 A:His240 2.00 Cu CD2 A:His240 4.14 Cu CE1 A:His240 3.02 Cu CG A:His240 2.98 Cu CA A:His240 3.84 Cu CG2 A:Val243 4.76 Cu CG2 A:Val287 4.95 Cu CA A:Trp288 4.98 Cu NE2 A:His290 2.02 Cu ND1 A:His290 4.07 Cu CD2 A:His290 3.04 Cu CE1 A:His290 2.93 Cu CG A:His290 4.15 Cu NE2 A:His291 1.95 Cu ND1 A:His291 4.07 Cu CD2 A:His291 2.87 Cu CE1 A:His291 2.98 Cu CG A:His291 4.03 Cu NA A:Hea516 4.62 Cu C2A A:Hea516 4.94 Cu C4A A:Hea516 4.85 Cu FE A:Hea516 4.91 Cu C1A A:Hea516 4.63 Cu O A:No520 2.50 Cu N A:No520 3.26 interactive model: Copper binding site 2 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3ag3. 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 4.68 Cu CD1 B:Trp104 4.47 Cu CZ2 B:Trp106 4.99 Cu O B:Leu160 4.81 Cu NE2 B:His161 4.19 Cu CB B:His161 3.60 Cu ND1 B:His161 2.06 Cu CD2 B:His161 4.28 Cu CE1 B:His161 3.04 Cu CG B:His161 3.17 Cu CA B:His161 4.27 Cu CB B:Cys196 3.52 Cu SG B:Cys196 2.29 Cu CA B:Cys196 4.88 Cu O B:Glu198 4.18 Cu CB B:Cys200 3.27 Cu SG B:Cys200 2.39 Cu CA B:Cys200 4.73 Cu ND1 B:His204 4.50 Cu CA B:His204 4.76 Cu CB B:Met207 4.93 Cu CE B:Met207 3.10 Cu CG B:Met207 3.48 Cu SD B:Met207 2.37 Cu CU1 B:Cua228 0.00 Cu CU2 B:Cua228 2.49 interactive model: Copper binding site 3 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3ag3. 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 ND1 B:His161 4.18 Cu CA B:His161 4.93 Cu O B:Cys196 4.23 Cu CB B:Cys196 3.34 Cu SG B:Cys196 2.32 Cu C B:Cys196 4.23 Cu CA B:Cys196 4.47 Cu N B:Ser197 4.62 Cu O B:Glu198 2.54 Cu N B:Glu198 4.19 Cu C B:Glu198 3.65 Cu CA B:Glu198 4.65 Cu N B:Ile199 4.41 Cu C B:Ile199 4.28 Cu CA B:Ile199 4.26 Cu N B:Cys200 3.67 Cu CB B:Cys200 3.39 Cu SG B:Cys200 2.27 Cu C B:Cys200 5.00 Cu CA B:Cys200 4.18 Cu O B:His204 3.88 Cu NE2 B:His204 4.13 Cu N B:His204 4.75 Cu CB B:His204 3.50 Cu ND1 B:His204 2.05 Cu CD2 B:His204 4.20 Cu C B:His204 4.17 Cu CE1 B:His204 2.98 Cu CG B:His204 3.07 Cu CA B:His204 3.55 Cu CG B:Met207 4.68 Cu SD B:Met207 4.35 Cu CU1 B:Cua228 2.49 Cu CU2 B:Cua228 0.00 interactive model: Copper binding site 4 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3ag3. 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: No520, conact list: Atom Atom Distance (A) Cu NE2 N:His240 4.10 Cu N N:His240 4.77 Cu CB N:His240 3.33 Cu ND1 N:His240 1.96 Cu CD2 N:His240 4.11 Cu CE1 N:His240 2.97 Cu CG N:His240 2.96 Cu CA N:His240 3.82 Cu CG2 N:Val243 4.74 Cu CG2 N:Val287 4.95 Cu NE2 N:His290 2.03 Cu ND1 N:His290 4.13 Cu CD2 N:His290 3.00 Cu CE1 N:His290 3.03 Cu CG N:His290 4.15 Cu NE2 N:His291 2.00 Cu ND1 N:His291 4.07 Cu CD2 N:His291 2.91 Cu CE1 N:His291 3.01 Cu CG N:His291 4.07 Cu NA N:Hea516 4.60 Cu C2A N:Hea516 4.95 Cu C4A N:Hea516 4.83 Cu FE N:Hea516 4.93 Cu C1A N:Hea516 4.63 Cu O N:No520 2.45 Cu N N:No520 3.30 interactive model: Copper binding site 5 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3ag3. 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 4.74 Cu CD1 O:Trp104 4.49 Cu O O:Leu160 4.79 Cu NE2 O:His161 4.23 Cu CB O:His161 3.58 Cu ND1 O:His161 2.11 Cu CD2 O:His161 4.31 Cu CE1 O:His161 3.04 Cu CG O:His161 3.21 Cu CA O:His161 4.22 Cu CB O:Cys196 3.57 Cu SG O:Cys196 2.34 Cu CA O:Cys196 4.97 Cu O O:Glu198 4.12 Cu N O:Cys200 4.90 Cu CB O:Cys200 3.27 Cu SG O:Cys200 2.37 Cu CA O:Cys200 4.67 Cu ND1 O:His204 4.47 Cu CA O:His204 4.74 Cu CB O:Met207 4.89 Cu CE O:Met207 3.14 Cu CG O:Met207 3.42 Cu SD O:Met207 2.39 Cu CU1 O:Cua228 0.00 Cu CU2 O:Cua228 2.51 interactive model: Copper binding site 6 out of 6 in 3ag3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3ag3. 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 5.00 Cu ND1 O:His161 4.22 Cu CA O:His161 4.87 Cu O O:Cys196 4.28 Cu CB O:Cys196 3.42 Cu SG O:Cys196 2.30 Cu C O:Cys196 4.31 Cu CA O:Cys196 4.53 Cu N O:Ser197 4.64 Cu O O:Glu198 2.44 Cu N O:Glu198 4.15 Cu C O:Glu198 3.59 Cu CA O:Glu198 4.57 Cu N O:Ile199 4.39 Cu C O:Ile199 4.24 Cu CA O:Ile199 4.27 Cu N O:Cys200 3.59 Cu CB O:Cys200 3.45 Cu SG O:Cys200 2.23 Cu CA O:Cys200 4.15 Cu O O:His204 3.90 Cu NE2 O:His204 4.06 Cu N O:His204 4.78 Cu CB O:His204 3.53 Cu ND1 O:His204 2.01 Cu CD2 O:His204 4.15 Cu C O:His204 4.17 Cu CE1 O:His204 2.89 Cu CG O:His204 3.09 Cu CA O:His204 3.54 Cu CG O:Met207 4.60 Cu SD O:Met207 4.39 Cu CU1 O:Cua228 2.51 Cu CU2 O:Cua228 0.00 interactive model: