Copper in the structure of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 (pdb 2e86)

The binding sites of Copper atom in the structure of Azide Bound to Copper Containing Nitrite Reductase From A. Faecalis S- 6 (pdb code 2e86). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2e86 structure was solved by E.I.TOCHEVA, M.E.P.MURPHY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.5 Space group P212121 a (A) 61.750 b (A) 102.582 c (A) 146.000 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.4 Rfree (%) 17.9 Copper Binding Sites: Copper binding site 1 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2e86. 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: Met62, A: Met94, A: His95, A: Asn96, A: Cys136, A: Pro138, A: His145, A: Met150, conact list: Atom Atom Distance (A) Cu CB A:Met62 4.73 Cu SD A:Met62 4.37 Cu O A:Met94 4.33 Cu NE2 A:His95 4.16 Cu N A:His95 4.89 Cu CB A:His95 3.48 Cu ND1 A:His95 2.10 Cu CD2 A:His95 4.23 Cu C A:His95 4.86 Cu CE1 A:His95 3.03 Cu CG A:His95 3.13 Cu CA A:His95 3.87 Cu N A:Asn96 4.67 Cu CB A:Cys136 3.17 Cu SG A:Cys136 2.23 Cu CA A:Cys136 4.62 Cu CD A:Pro138 4.64 Cu CG A:Pro138 4.31 Cu NE2 A:His145 4.08 Cu CB A:His145 3.55 Cu ND1 A:His145 2.08 Cu CD2 A:His145 4.19 Cu CE1 A:His145 2.95 Cu CG A:His145 3.13 Cu CA A:His145 4.75 Cu CB A:Met150 4.30 Cu CE A:Met150 3.24 Cu CG A:Met150 3.82 Cu SD A:Met150 2.47 interactive model: Copper binding site 2 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2e86. 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: Asp98, A: His100, A: His135, B: His255, B: His306, B: Leu308, A: Azi503, B: Hoh2233, conact list: Atom Atom Distance (A) Cu OD2 A:Asp98 4.72 Cu OD1 A:Asp98 3.63 Cu CG A:Asp98 4.30 Cu NE2 A:His100 2.03 Cu ND1 A:His100 4.07 Cu CD2 A:His100 3.12 Cu CE1 A:His100 2.91 Cu CG A:His100 4.20 Cu NE2 A:His135 2.04 Cu ND1 A:His135 4.15 Cu CD2 A:His135 2.98 Cu CE1 A:His135 3.06 Cu CG A:His135 4.14 Cu NE2 B:His255 4.17 Cu ND1 B:His255 4.81 Cu CD2 B:His255 4.55 Cu CE1 B:His255 4.36 Cu CG B:His255 4.95 Cu NE2 B:His306 2.08 Cu ND1 B:His306 4.14 Cu CD2 B:His306 3.13 Cu CE1 B:His306 2.99 Cu CG B:His306 4.24 Cu CD1 B:Leu308 4.99 Cu CD2 B:Leu308 4.85 Cu N1 A:Azi503 3.71 Cu N3 A:Azi503 1.97 Cu N2 A:Azi503 2.70 Cu O B:Hoh2233 4.87 interactive model: Copper binding site 3 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2e86. 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: Met62, B: Met94, B: His95, B: Asn96, B: Cys136, B: Pro138, B: His145, B: Met150, conact list: Atom Atom Distance (A) Cu CB B:Met62 4.81 Cu SD B:Met62 4.36 Cu O B:Met94 4.27 Cu C B:Met94 4.98 Cu NE2 B:His95 4.14 Cu N B:His95 4.86 Cu CB B:His95 3.49 Cu ND1 B:His95 2.07 Cu CD2 B:His95 4.22 Cu C B:His95 4.86 Cu CE1 B:His95 3.00 Cu CG B:His95 3.12 Cu CA B:His95 3.86 Cu N B:Asn96 4.67 Cu CB B:Cys136 3.15 Cu SG B:Cys136 2.24 Cu CA B:Cys136 4.59 Cu CD B:Pro138 4.60 Cu CG B:Pro138 4.22 Cu NE2 B:His145 4.15 Cu CB B:His145 3.58 Cu ND1 B:His145 2.12 Cu CD2 B:His145 4.25 Cu CE1 B:His145 3.00 Cu CG B:His145 3.18 Cu CA B:His145 4.81 Cu CB B:Met150 4.38 Cu CE B:Met150 3.22 Cu CG B:Met150 3.90 Cu SD B:Met150 2.49 interactive model: Copper binding site 4 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2e86. 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: Asp98, B: His100, B: His135, C: His255, C: His306, C: Leu308, C: Azi2013, B: Hoh2397, C: Hoh2206, conact list: Atom Atom Distance (A) Cu OD2 B:Asp98 4.78 Cu OD1 B:Asp98 3.60 Cu CG B:Asp98 4.30 Cu NE2 B:His100 2.04 Cu ND1 B:His100 4.09 Cu CD2 B:His100 3.12 Cu CE1 B:His100 2.93 Cu CG B:His100 4.21 Cu NE2 B:His135 2.03 Cu ND1 B:His135 4.15 Cu CD2 B:His135 2.97 Cu CE1 B:His135 3.07 Cu CG B:His135 4.14 Cu NE2 C:His255 4.13 Cu ND1 C:His255 4.80 Cu CD2 C:His255 4.49 Cu CE1 C:His255 4.35 Cu CG C:His255 4.89 Cu NE2 C:His306 2.08 Cu ND1 C:His306 4.14 Cu CD2 C:His306 3.13 Cu CE1 C:His306 2.99 Cu CG C:His306 4.24 Cu CD1 C:Leu308 4.98 Cu CD2 C:Leu308 4.97 Cu N1 C:Azi2013 3.84 Cu N3 C:Azi2013 2.08 Cu N2 C:Azi2013 2.79 Cu O B:Hoh2397 4.57 Cu O C:Hoh2206 4.86 interactive model: Copper binding site 5 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2e86. 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: Met62, C: Met94, C: His95, C: Asn96, C: Cys136, C: Pro138, C: His145, C: Met150, conact list: Atom Atom Distance (A) Cu CB C:Met62 4.73 Cu SD C:Met62 4.44 Cu O C:Met94 4.27 Cu C C:Met94 4.97 Cu NE2 C:His95 4.17 Cu N C:His95 4.85 Cu CB C:His95 3.48 Cu ND1 C:His95 2.10 Cu CD2 C:His95 4.24 Cu C C:His95 4.84 Cu CE1 C:His95 3.04 Cu CG C:His95 3.13 Cu CA C:His95 3.85 Cu N C:Asn96 4.66 Cu CB C:Cys136 3.14 Cu SG C:Cys136 2.23 Cu CA C:Cys136 4.59 Cu CD C:Pro138 4.62 Cu CG C:Pro138 4.24 Cu NE2 C:His145 4.16 Cu CB C:His145 3.55 Cu ND1 C:His145 2.14 Cu CD2 C:His145 4.24 Cu CE1 C:His145 3.03 Cu CG C:His145 3.17 Cu CA C:His145 4.78 Cu CB C:Met150 4.36 Cu CE C:Met150 3.27 Cu CG C:Met150 3.85 Cu SD C:Met150 2.48 interactive model: Copper binding site 6 out of 6 in 2e86 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2e86. 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: His255, A: His306, A: Leu308, C: Asp98, C: His100, C: His135, C: Azi503, A: Hoh2247, C: Hoh2336, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.13 Cu ND1 A:His255 4.79 Cu CD2 A:His255 4.49 Cu CE1 A:His255 4.35 Cu CG A:His255 4.89 Cu NE2 A:His306 2.08 Cu ND1 A:His306 4.13 Cu CD2 A:His306 3.16 Cu CE1 A:His306 2.97 Cu CG A:His306 4.25 Cu CD1 A:Leu308 4.93 Cu CD2 A:Leu308 4.91 Cu OD2 C:Asp98 4.86 Cu OD1 C:Asp98 3.56 Cu CG C:Asp98 4.36 Cu NE2 C:His100 2.01 Cu ND1 C:His100 4.05 Cu CD2 C:His100 3.11 Cu CE1 C:His100 2.89 Cu CG C:His100 4.19 Cu NE2 C:His135 2.03 Cu ND1 C:His135 4.14 Cu CD2 C:His135 2.97 Cu CE1 C:His135 3.06 Cu CG C:His135 4.13 Cu N1 C:Azi503 3.94 Cu N3 C:Azi503 2.08 Cu N2 C:Azi503 2.94 Cu O A:Hoh2247 4.89 Cu O C:Hoh2336 4.46 interactive model: