Copper in the structure of Wild-Type Plastocyanin From Silene (pdb 1byo)

The binding sites of Copper atom in the structure of Wild-Type Plastocyanin From Silene (pdb code 1byo). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1byo structure was solved by H.SUGAWARA, T.INOUE, C.LI, M.GOTOWDA, T.HIBINO, T.TAKABE, Y.KAI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.0 Space group P3221 a (A) 76.600 b (A) 76.600 c (A) 65.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.7 Rfree (%) 22.5 Copper Binding Sites: Copper binding site 1 out of 2 in 1byo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1byo. 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: Gly34, A: Pro36, A: His37, A: Asn38, A: Cys84, A: Pro86, A: His87, A: Met92, conact list: Atom Atom Distance (A) Cu O A:Gly34 4.99 Cu O A:Pro36 3.40 Cu C A:Pro36 4.29 Cu NE2 A:His37 4.08 Cu N A:His37 4.39 Cu CB A:His37 3.45 Cu ND1 A:His37 2.02 Cu CD2 A:His37 4.17 Cu C A:His37 4.73 Cu CE1 A:His37 2.95 Cu CG A:His37 3.06 Cu CA A:His37 3.58 Cu N A:Asn38 4.66 Cu CB A:Cys84 3.36 Cu SG A:Cys84 2.19 Cu CA A:Cys84 4.75 Cu CB A:Pro86 4.95 Cu NE2 A:His87 4.10 Cu N A:His87 4.40 Cu CB A:His87 3.44 Cu ND1 A:His87 2.05 Cu CD2 A:His87 4.16 Cu CE1 A:His87 2.99 Cu CG A:His87 3.04 Cu CA A:His87 4.59 Cu CB A:Met92 4.64 Cu CE A:Met92 3.50 Cu CG A:Met92 4.14 Cu SD A:Met92 2.74 interactive model: Copper binding site 2 out of 2 in 1byo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1byo. 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: Gly34, B: Pro36, B: His37, B: Asn38, B: Cys84, B: Pro86, B: His87, B: Met92, conact list: Atom Atom Distance (A) Cu O B:Gly34 4.96 Cu O B:Pro36 3.57 Cu C B:Pro36 4.39 Cu NE2 B:His37 3.98 Cu N B:His37 4.43 Cu CB B:His37 3.35 Cu ND1 B:His37 1.90 Cu CD2 B:His37 4.05 Cu C B:His37 4.69 Cu CE1 B:His37 2.86 Cu CG B:His37 2.94 Cu CA B:His37 3.58 Cu N B:Asn38 4.58 Cu O B:Cys84 4.98 Cu CB B:Cys84 3.29 Cu SG B:Cys84 2.11 Cu C B:Cys84 4.95 Cu CA B:Cys84 4.67 Cu CG B:Pro86 4.54 Cu NE2 B:His87 4.41 Cu N B:His87 4.47 Cu CB B:His87 3.46 Cu ND1 B:His87 2.31 Cu CD2 B:His87 4.40 Cu CE1 B:His87 3.31 Cu CG B:His87 3.22 Cu CA B:His87 4.59 Cu CB B:Met92 4.59 Cu CE B:Met92 3.60 Cu CG B:Met92 4.20 Cu SD B:Met92 2.79 interactive model: