Copper in the structure of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea (pdb 1iby)

The binding sites of Copper atom in the structure of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea (pdb code 1iby). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1iby structure was solved by R.L.LIEBERMAN, D.M.ARCIERO, A.B.HOOPER, A.C.ROSENZWEIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-1.6 Space group H32 a (A) 96.378 b (A) 96.378 c (A) 279.772 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.6 Rfree (%) 21.6 Copper Binding Sites: Copper binding site 1 out of 4 in 1iby Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1iby. 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: Val33, A: Glu60, A: Gly61, A: Cys95, A: Leu97, A: His98, A: His103, A: Hez1169, A: Hoh1238, conact list: Atom Atom Distance (A) Cu CB A:Val33 4.62 Cu CG2 A:Val33 4.81 Cu CG1 A:Val33 4.44 Cu OE1 A:Glu60 2.05 Cu CB A:Glu60 4.47 Cu OE2 A:Glu60 3.76 Cu CD A:Glu60 3.21 Cu C A:Glu60 4.83 Cu CG A:Glu60 4.41 Cu CA A:Glu60 4.41 Cu O A:Gly61 4.91 Cu N A:Gly61 4.13 Cu CB A:Cys95 3.18 Cu SG A:Cys95 2.26 Cu CA A:Cys95 4.61 Cu CB A:Leu97 4.82 Cu NE2 A:His98 4.01 Cu N A:His98 4.30 Cu CB A:His98 3.62 Cu ND1 A:His98 2.01 Cu CD2 A:His98 4.17 Cu CE1 A:His98 2.83 Cu CG A:His98 3.14 Cu CA A:His98 4.61 Cu NE2 A:His103 4.07 Cu CB A:His103 3.31 Cu ND1 A:His103 1.98 Cu CD2 A:His103 4.10 Cu CE1 A:His103 2.97 Cu CG A:His103 2.97 Cu CA A:His103 4.78 Cu O6 A:Hez1169 4.45 Cu O A:Hoh1238 2.06 interactive model: Copper binding site 2 out of 4 in 1iby Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1iby. 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: Val33, B: Glu60, B: Gly61, B: Cys95, B: Leu97, B: His98, B: His103, B: Hez1170, B: Hoh1310, conact list: Atom Atom Distance (A) Cu CB B:Val33 4.91 Cu CG1 B:Val33 4.68 Cu OE1 B:Glu60 2.11 Cu CB B:Glu60 4.60 Cu OE2 B:Glu60 3.71 Cu CD B:Glu60 3.23 Cu C B:Glu60 4.93 Cu CG B:Glu60 4.48 Cu CA B:Glu60 4.50 Cu O B:Gly61 4.96 Cu N B:Gly61 4.21 Cu CB B:Cys95 3.19 Cu SG B:Cys95 2.29 Cu CA B:Cys95 4.62 Cu CB B:Leu97 4.92 Cu NE2 B:His98 4.10 Cu N B:His98 4.32 Cu CB B:His98 3.52 Cu ND1 B:His98 2.06 Cu CD2 B:His98 4.21 Cu CE1 B:His98 2.95 Cu CG B:His98 3.13 Cu CA B:His98 4.56 Cu NE2 B:His103 4.06 Cu CB B:His103 3.32 Cu ND1 B:His103 1.97 Cu CD2 B:His103 4.09 Cu CE1 B:His103 2.95 Cu CG B:His103 2.97 Cu CA B:His103 4.81 Cu O6 B:Hez1170 4.66 Cu O B:Hoh1310 2.42 interactive model: Copper binding site 3 out of 4 in 1iby Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1iby. 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: Val33, C: Glu60, C: Gly61, C: Cys95, C: Leu97, C: His98, C: His103, C: Hez1172, C: Hoh1269, conact list: Atom Atom Distance (A) Cu CB C:Val33 4.85 Cu CG1 C:Val33 4.60 Cu OE1 C:Glu60 2.10 Cu CB C:Glu60 4.57 Cu OE2 C:Glu60 3.73 Cu CD C:Glu60 3.23 Cu C C:Glu60 4.93 Cu CG C:Glu60 4.48 Cu CA C:Glu60 4.51 Cu O C:Gly61 4.92 Cu N C:Gly61 4.22 Cu CB C:Cys95 3.18 Cu SG C:Cys95 2.25 Cu CA C:Cys95 4.60 Cu CB C:Leu97 4.89 Cu NE2 C:His98 4.01 Cu N C:His98 4.23 Cu CB C:His98 3.47 Cu ND1 C:His98 1.98 Cu CD2 C:His98 4.12 Cu CE1 C:His98 2.87 Cu CG C:His98 3.05 Cu CA C:His98 4.48 Cu NE2 C:His103 4.08 Cu CB C:His103 3.31 Cu ND1 C:His103 1.98 Cu CD2 C:His103 4.10 Cu CE1 C:His103 2.97 Cu CG C:His103 2.98 Cu CA C:His103 4.79 Cu O1 C:Hez1172 4.19 Cu O C:Hoh1269 2.38 interactive model: Copper binding site 4 out of 4 in 1iby Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1iby. 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: Val33, D: Glu60, D: Gly61, D: Cys95, D: Leu97, D: His98, D: His103, D: Hez1171, D: Hoh1270, conact list: Atom Atom Distance (A) Cu CB D:Val33 4.76 Cu CG1 D:Val33 4.59 Cu OE1 D:Glu60 2.11 Cu CB D:Glu60 4.56 Cu OE2 D:Glu60 3.77 Cu CD D:Glu60 3.26 Cu C D:Glu60 4.92 Cu CG D:Glu60 4.48 Cu CA D:Glu60 4.49 Cu O D:Gly61 4.98 Cu N D:Gly61 4.21 Cu CB D:Cys95 3.19 Cu SG D:Cys95 2.27 Cu CA D:Cys95 4.62 Cu CB D:Leu97 4.82 Cu NE2 D:His98 4.03 Cu N D:His98 4.30 Cu CB D:His98 3.60 Cu ND1 D:His98 2.02 Cu CD2 D:His98 4.18 Cu CE1 D:His98 2.86 Cu CG D:His98 3.13 Cu CA D:His98 4.58 Cu NE2 D:His103 4.05 Cu CB D:His103 3.28 Cu ND1 D:His103 1.95 Cu CD2 D:His103 4.07 Cu CE1 D:His103 2.94 Cu CG D:His103 2.94 Cu CA D:His103 4.76 Cu O1 D:Hez1171 4.31 Cu O D:Hoh1270 2.15 interactive model: