Copper in the structure of Copper-Bound C-Terminal Domain of Nikr (pdb 3bkt)

The binding sites of Copper atom in the structure of Copper-Bound C-Terminal Domain of Nikr (pdb code 3bkt). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 3bkt structure was solved by C.M.PHILLIPS, E.R.SCHREITER, C.L.DRENNAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.2-1.5 Space group P212121 a (A) 45.949 b (A) 78.442 c (A) 81.460 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 22.7 Copper Binding Sites: Copper binding site 1 out of 4 in 3bkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 3bkt. 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: His62, A: His87, A: Val88, A: His89, A: Asp94, A: Cys95, C: Val72, C: His76, conact list: Atom Atom Distance (A) Cu CB A:His62 4.73 Cu NE2 A:His87 2.01 Cu ND1 A:His87 4.07 Cu CD2 A:His87 3.06 Cu CE1 A:His87 2.92 Cu CG A:His87 4.16 Cu O A:Val88 4.37 Cu C A:Val88 4.61 Cu NE2 A:His89 4.40 Cu N A:His89 4.35 Cu CB A:His89 3.88 Cu ND1 A:His89 2.39 Cu CD2 A:His89 4.56 Cu CE1 A:His89 3.20 Cu CG A:His89 3.49 Cu CA A:His89 3.81 Cu O A:Asp94 4.49 Cu C A:Asp94 4.84 Cu N A:Cys95 4.60 Cu CB A:Cys95 3.32 Cu SG A:Cys95 2.37 Cu CA A:Cys95 3.88 Cu CG2 C:Val72 3.89 Cu NE2 C:His76 1.99 Cu ND1 C:His76 4.00 Cu CD2 C:His76 3.04 Cu CE1 C:His76 2.87 Cu CG C:His76 4.11 interactive model: Copper binding site 2 out of 4 in 3bkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 3bkt. 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: His62, B: His87, B: Val88, B: His89, B: Asp94, B: Cys95, D: Val72, D: His76, conact list: Atom Atom Distance (A) Cu CB B:His62 4.90 Cu NE2 B:His87 2.07 Cu ND1 B:His87 4.15 Cu CD2 B:His87 3.10 Cu CE1 B:His87 3.02 Cu CG B:His87 4.22 Cu O B:Val88 4.43 Cu C B:Val88 4.65 Cu NE2 B:His89 4.18 Cu N B:His89 4.41 Cu CB B:His89 3.86 Cu ND1 B:His89 2.24 Cu CD2 B:His89 4.38 Cu CE1 B:His89 2.99 Cu CG B:His89 3.37 Cu CA B:His89 3.89 Cu O B:Asp94 4.54 Cu C B:Asp94 4.82 Cu N B:Cys95 4.53 Cu CB B:Cys95 3.29 Cu SG B:Cys95 2.43 Cu CA B:Cys95 3.83 Cu CB D:Val72 4.80 Cu CG1 D:Val72 3.34 Cu NE2 D:His76 1.96 Cu ND1 D:His76 4.06 Cu CD2 D:His76 2.91 Cu CE1 D:His76 2.98 Cu CG D:His76 4.06 interactive model: Copper binding site 3 out of 4 in 3bkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 3bkt. 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: Val72, A: His76, C: His62, C: His87, C: Val88, C: His89, C: Asp94, C: Cys95, conact list: Atom Atom Distance (A) Cu CB A:Val72 4.91 Cu CB A:Val72 4.90 Cu CG2 A:Val72 3.49 Cu CG1 A:Val72 3.41 Cu NE2 A:His76 2.11 Cu ND1 A:His76 4.19 Cu CD2 A:His76 3.07 Cu CE1 A:His76 3.09 Cu CG A:His76 4.21 Cu CD2 C:His62 4.56 Cu CG C:His62 4.94 Cu NE2 C:His87 2.07 Cu ND1 C:His87 4.10 Cu CD2 C:His87 3.16 Cu CE1 C:His87 2.94 Cu CG C:His87 4.24 Cu O C:Val88 4.46 Cu C C:Val88 4.67 Cu NE2 C:His89 4.50 Cu N C:His89 4.52 Cu CB C:His89 4.12 Cu ND1 C:His89 2.54 Cu CD2 C:His89 4.72 Cu CE1 C:His89 3.27 Cu CG C:His89 3.69 Cu CA C:His89 4.05 Cu O C:Asp94 4.49 Cu C C:Asp94 4.76 Cu N C:Cys95 4.49 Cu CB C:Cys95 3.33 Cu SG C:Cys95 2.48 Cu CA C:Cys95 3.83 interactive model: Copper binding site 4 out of 4 in 3bkt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 3bkt. 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: Val72, B: His76, D: His62, D: His87, D: Val88, D: His89, D: Asp94, D: Cys95, conact list: Atom Atom Distance (A) Cu CG2 B:Val72 3.55 Cu CG1 B:Val72 3.73 Cu NE2 B:His76 2.01 Cu ND1 B:His76 4.09 Cu CD2 B:His76 3.06 Cu CE1 B:His76 2.95 Cu CG B:His76 4.16 Cu CD2 D:His62 4.69 Cu NE2 D:His87 2.02 Cu ND1 D:His87 4.07 Cu CD2 D:His87 3.10 Cu CE1 D:His87 2.92 Cu CG D:His87 4.19 Cu O D:Val88 4.37 Cu C D:Val88 4.65 Cu NE2 D:His89 4.45 Cu N D:His89 4.49 Cu CB D:His89 3.98 Cu ND1 D:His89 2.48 Cu CD2 D:His89 4.63 Cu CE1 D:His89 3.26 Cu CG D:His89 3.58 Cu CA D:His89 3.91 Cu O D:Asp94 4.50 Cu C D:Asp94 4.81 Cu N D:Cys95 4.53 Cu CB D:Cys95 3.28 Cu SG D:Cys95 2.41 Cu CA D:Cys95 3.82 interactive model: