Copper in the structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides With K362M Mutation (pdb 3oma)

The binding sites of Copper atom in the structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides With K362M Mutation (pdb code 3oma). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3oma structure was solved by J.LIU, L.QIN, S.FERGUSON-MILLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.3 Space group P212121 a (A) 125.019 b (A) 131.579 c (A) 176.626 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.1 Rfree (%) 21.9 Copper Binding Sites: Copper binding site 1 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3oma. 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: His284, A: His333, A: His334, A: Oh706, A: Hea2, A: Hoh727, A: Hoh806, conact list: Atom Atom Distance (A) Cu NE2 A:His284 4.22 Cu N A:His284 4.61 Cu CB A:His284 3.21 Cu ND1 A:His284 2.13 Cu CD2 A:His284 4.15 Cu CE1 A:His284 3.14 Cu CG A:His284 3.00 Cu CA A:His284 3.84 Cu NE2 A:His333 2.04 Cu ND1 A:His333 4.07 Cu CD2 A:His333 3.12 Cu CE1 A:His333 2.92 Cu CG A:His333 4.19 Cu NE2 A:His334 2.09 Cu ND1 A:His334 4.07 Cu CD2 A:His334 3.01 Cu CE1 A:His334 3.01 Cu CG A:His334 4.11 Cu O A:Oh706 2.36 Cu NA A:Hea2 4.53 Cu C2A A:Hea2 4.92 Cu C4A A:Hea2 4.72 Cu C3A A:Hea2 4.96 Cu FE A:Hea2 4.97 Cu C1A A:Hea2 4.65 Cu O A:Hoh727 2.95 Cu O A:Hoh806 4.79 interactive model: Copper binding site 2 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3oma. 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: His217, B: Cys252, B: Ser253, B: Glu254, B: Leu255, B: Cys256, B: His260, B: Met263, B: Cu1288, conact list: Atom Atom Distance (A) Cu ND1 B:His217 4.24 Cu CA B:His217 4.97 Cu O B:Cys252 4.16 Cu CB B:Cys252 3.25 Cu SG B:Cys252 2.23 Cu C B:Cys252 4.15 Cu CA B:Cys252 4.32 Cu N B:Ser253 4.62 Cu O B:Glu254 2.56 Cu N B:Glu254 4.11 Cu C B:Glu254 3.51 Cu CA B:Glu254 4.45 Cu N B:Leu255 4.21 Cu C B:Leu255 4.22 Cu CA B:Leu255 4.14 Cu N B:Cys256 3.72 Cu CB B:Cys256 3.39 Cu SG B:Cys256 2.27 Cu CA B:Cys256 4.20 Cu O B:His260 3.97 Cu NE2 B:His260 4.03 Cu N B:His260 4.81 Cu CB B:His260 3.66 Cu ND1 B:His260 2.06 Cu CD2 B:His260 4.20 Cu C B:His260 4.26 Cu CE1 B:His260 2.86 Cu CG B:His260 3.18 Cu CA B:His260 3.63 Cu CG B:Met263 4.77 Cu SD B:Met263 4.49 Cu CU B:Cu1288 2.55 interactive model: Copper binding site 3 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3oma. 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: Tyr141, B: Trp143, B: His217, B: Cys252, B: Glu254, B: Cys256, B: His260, B: Met263, B: Cu287, conact list: Atom Atom Distance (A) Cu O B:Tyr141 4.62 Cu CD1 B:Trp143 4.50 Cu NE2 B:His217 4.13 Cu CB B:His217 3.71 Cu ND1 B:His217 2.13 Cu CD2 B:His217 4.30 Cu CE1 B:His217 2.94 Cu CG B:His217 3.26 Cu CA B:His217 4.29 Cu CB B:Cys252 3.44 Cu SG B:Cys252 2.29 Cu CA B:Cys252 4.83 Cu O B:Glu254 4.25 Cu CB B:Cys256 3.32 Cu SG B:Cys256 2.34 Cu CA B:Cys256 4.74 Cu ND1 B:His260 4.50 Cu CA B:His260 4.74 Cu CB B:Met263 4.92 Cu CE B:Met263 3.08 Cu CG B:Met263 3.53 Cu SD B:Met263 2.45 Cu CU B:Cu287 2.55 interactive model: Copper binding site 4 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3oma. 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: C: His284, C: His333, C: His334, C: Oh706, C: Hea2, C: Hoh556, conact list: Atom Atom Distance (A) Cu NE2 C:His284 4.17 Cu N C:His284 4.72 Cu CB C:His284 3.33 Cu ND1 C:His284 2.09 Cu CD2 C:His284 4.15 Cu CE1 C:His284 3.06 Cu CG C:His284 3.04 Cu CA C:His284 3.93 Cu NE2 C:His333 2.14 Cu ND1 C:His333 4.21 Cu CD2 C:His333 3.17 Cu CE1 C:His333 3.07 Cu CG C:His333 4.29 Cu NE2 C:His334 2.12 Cu ND1 C:His334 4.12 Cu CD2 C:His334 3.02 Cu CE1 C:His334 3.07 Cu CG C:His334 4.13 Cu O C:Oh706 2.30 Cu NA C:Hea2 4.54 Cu C2A C:Hea2 4.88 Cu C4A C:Hea2 4.72 Cu C3A C:Hea2 4.93 Cu FE C:Hea2 4.90 Cu C1A C:Hea2 4.63 Cu O C:Hoh556 2.96 interactive model: Copper binding site 5 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 3oma. 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: D: His217, D: Cys252, D: Ser253, D: Glu254, D: Leu255, D: Cys256, D: His260, D: Met263, D: Cu1287, conact list: Atom Atom Distance (A) Cu ND1 D:His217 4.28 Cu CA D:His217 4.94 Cu O D:Cys252 4.28 Cu CB D:Cys252 3.25 Cu SG D:Cys252 2.31 Cu C D:Cys252 4.16 Cu CA D:Cys252 4.33 Cu N D:Ser253 4.47 Cu O D:Glu254 2.63 Cu N D:Glu254 4.10 Cu C D:Glu254 3.57 Cu CA D:Glu254 4.49 Cu N D:Leu255 4.27 Cu C D:Leu255 4.27 Cu CA D:Leu255 4.26 Cu N D:Cys256 3.75 Cu CB D:Cys256 3.41 Cu SG D:Cys256 2.32 Cu CA D:Cys256 4.22 Cu O D:His260 3.90 Cu NE2 D:His260 3.97 Cu N D:His260 4.78 Cu CB D:His260 3.64 Cu ND1 D:His260 1.99 Cu CD2 D:His260 4.14 Cu C D:His260 4.21 Cu CE1 D:His260 2.79 Cu CG D:His260 3.12 Cu CA D:His260 3.60 Cu CG D:Met263 4.68 Cu SD D:Met263 4.46 Cu CU D:Cu1287 2.55 interactive model: Copper binding site 6 out of 6 in 3oma Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 3oma. 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: D: Tyr141, D: Trp143, D: Trp145, D: His217, D: Cys252, D: Glu254, D: Cys256, D: His260, D: Met263, D: Cu286, conact list: Atom Atom Distance (A) Cu O D:Tyr141 4.71 Cu CD1 D:Trp143 4.46 Cu CZ2 D:Trp145 4.97 Cu NE2 D:His217 4.23 Cu CB D:His217 3.60 Cu ND1 D:His217 2.18 Cu CD2 D:His217 4.32 Cu CE1 D:His217 3.08 Cu CG D:His217 3.23 Cu CA D:His217 4.25 Cu CB D:Cys252 3.45 Cu SG D:Cys252 2.38 Cu CA D:Cys252 4.85 Cu O D:Glu254 4.27 Cu CB D:Cys256 3.34 Cu SG D:Cys256 2.32 Cu CA D:Cys256 4.76 Cu ND1 D:His260 4.46 Cu CA D:His260 4.76 Cu CB D:Met263 4.87 Cu CE D:Met263 3.08 Cu CG D:Met263 3.43 Cu SD D:Met263 2.37 Cu CU D:Cu286 2.55 interactive model: