Copper in the structure of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase At Cryo Temperature (pdb 1as8)

The binding sites of Copper atom in the structure of Structure of Nitrite Bound to Reduced Alcaligenes Faecalis Nitrite Reductase At Cryo Temperature (pdb code 1as8). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1as8 structure was solved by M.E.P.MURPHY, E.T.ADMAN, S.TURLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.9 Space group P212121 a (A) 61.100 b (A) 102.800 c (A) 146.300 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) n/a Copper Binding Sites: Copper binding site 1 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1as8. 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 4.88 Cu SD A:Met62 4.46 Cu O A:Met94 4.32 Cu NE2 A:His95 4.18 Cu N A:His95 4.94 Cu CB A:His95 3.49 Cu ND1 A:His95 2.07 Cu CD2 A:His95 4.24 Cu C A:His95 4.92 Cu CE1 A:His95 3.01 Cu CG A:His95 3.12 Cu CA A:His95 3.90 Cu N A:Asn96 4.75 Cu H A:Asn96 3.96 Cu CB A:Cys136 3.09 Cu SG A:Cys136 2.06 Cu CA A:Cys136 4.51 Cu CD A:Pro138 4.42 Cu CG A:Pro138 4.17 Cu NE2 A:His145 4.19 Cu CB A:His145 3.45 Cu ND1 A:His145 2.07 Cu CD2 A:His145 4.23 Cu CE1 A:His145 3.03 Cu CG A:His145 3.10 Cu CA A:His145 4.67 Cu CB A:Met150 4.29 Cu CE A:Met150 3.29 Cu CG A:Met150 3.77 Cu SD A:Met150 2.58 interactive model: Copper binding site 2 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1as8. 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, A: No2503, A: Hoh754, conact list: Atom Atom Distance (A) Cu OD2 A:Asp98 4.88 Cu OD1 A:Asp98 3.62 Cu CG A:Asp98 4.38 Cu NE2 A:His100 1.99 Cu ND1 A:His100 4.08 Cu CD2 A:His100 3.13 Cu CE1 A:His100 2.88 Cu HD1 A:His100 4.89 Cu CG A:His100 4.22 Cu NE2 A:His135 1.89 Cu ND1 A:His135 4.01 Cu CD2 A:His135 2.99 Cu CE1 A:His135 2.84 Cu HD1 A:His135 4.88 Cu CG A:His135 4.10 Cu NE2 B:His255 4.09 Cu ND1 B:His255 4.94 Cu CD2 B:His255 4.41 Cu CE1 B:His255 4.45 Cu HE2 B:His255 3.76 Cu CG B:His255 4.94 Cu NE2 B:His306 2.11 Cu ND1 B:His306 4.17 Cu CD2 B:His306 3.28 Cu CE1 B:His306 2.94 Cu HD1 B:His306 4.98 Cu CG B:His306 4.34 Cu O1 A:No2503 2.67 Cu O2 A:No2503 2.23 Cu N A:No2503 2.46 Cu O A:Hoh754 4.60 Cu H1 A:Hoh754 4.86 Cu H2 A:Hoh754 3.62 interactive model: Copper binding site 3 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1as8. 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 4.97 Cu SD B:Met62 4.39 Cu O B:Met94 4.27 Cu C B:Met94 4.95 Cu NE2 B:His95 4.22 Cu N B:His95 4.82 Cu CB B:His95 3.40 Cu ND1 B:His95 2.06 Cu CD2 B:His95 4.24 Cu C B:His95 4.82 Cu CE1 B:His95 3.06 Cu CG B:His95 3.08 Cu CA B:His95 3.79 Cu N B:Asn96 4.70 Cu H B:Asn96 3.93 Cu CB B:Cys136 3.18 Cu SG B:Cys136 2.15 Cu CA B:Cys136 4.60 Cu CD B:Pro138 4.46 Cu CG B:Pro138 3.97 Cu NE2 B:His145 4.08 Cu CB B:His145 3.60 Cu ND1 B:His145 1.99 Cu CD2 B:His145 4.20 Cu CE1 B:His145 2.87 Cu CG B:His145 3.12 Cu HE2 B:His145 4.94 Cu CA B:His145 4.81 Cu CB B:Met150 4.44 Cu CE B:Met150 3.36 Cu CG B:Met150 4.03 Cu SD B:Met150 2.66 interactive model: Copper binding site 4 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1as8. 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, B: No2503, B: Hoh640, B: Hoh728, conact list: Atom Atom Distance (A) Cu OD2 B:Asp98 4.90 Cu OD1 B:Asp98 3.53 Cu CG B:Asp98 4.38 Cu NE2 B:His100 1.94 Cu ND1 B:His100 3.96 Cu CD2 B:His100 3.15 Cu CE1 B:His100 2.72 Cu HD1 B:His100 4.75 Cu CG B:His100 4.18 Cu NE2 B:His135 2.00 Cu ND1 B:His135 4.15 Cu CD2 B:His135 3.01 Cu CE1 B:His135 3.02 Cu CG B:His135 4.17 Cu NE2 C:His255 4.00 Cu CD2 C:His255 4.25 Cu CE1 C:His255 4.52 Cu HE2 C:His255 3.65 Cu CG C:His255 4.89 Cu NE2 C:His306 2.13 Cu ND1 C:His306 4.21 Cu CD2 C:His306 3.27 Cu CE1 C:His306 3.00 Cu CG C:His306 4.35 Cu O1 B:No2503 2.21 Cu O2 B:No2503 2.38 Cu N B:No2503 2.45 Cu H2 B:Hoh640 4.31 Cu O B:Hoh728 4.61 Cu H1 B:Hoh728 4.75 interactive model: Copper binding site 5 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1as8. 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 4.71 Cu SD C:Met62 4.37 Cu O C:Met94 4.26 Cu NE2 C:His95 4.28 Cu N C:His95 4.89 Cu CB C:His95 3.56 Cu ND1 C:His95 2.16 Cu CD2 C:His95 4.34 Cu C C:His95 4.87 Cu CE1 C:His95 3.10 Cu CG C:His95 3.21 Cu CA C:His95 3.87 Cu N C:Asn96 4.72 Cu H C:Asn96 3.93 Cu CB C:Cys136 3.17 Cu SG C:Cys136 2.25 Cu CA C:Cys136 4.60 Cu CD C:Pro138 4.52 Cu CG C:Pro138 4.02 Cu NE2 C:His145 4.16 Cu CB C:His145 3.53 Cu ND1 C:His145 2.04 Cu CD2 C:His145 4.23 Cu CE1 C:His145 2.97 Cu CG C:His145 3.12 Cu CA C:His145 4.78 Cu CB C:Met150 4.41 Cu CE C:Met150 3.41 Cu CG C:Met150 3.86 Cu SD C:Met150 2.54 interactive model: Copper binding site 6 out of 6 in 1as8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1as8. 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: No2503, A: Hoh544, C: Hoh638, C: Hoh737, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.18 Cu ND1 A:His255 4.89 Cu CD2 A:His255 4.50 Cu CE1 A:His255 4.46 Cu HE2 A:His255 4.09 Cu CG A:His255 4.94 Cu NE2 A:His306 2.11 Cu ND1 A:His306 4.14 Cu CD2 A:His306 3.30 Cu CE1 A:His306 2.90 Cu HD1 A:His306 4.95 Cu CG A:His306 4.35 Cu CD1 A:Leu308 4.97 Cu OD2 C:Asp98 4.93 Cu OD1 C:Asp98 3.69 Cu CG C:Asp98 4.47 Cu NE2 C:His100 1.84 Cu ND1 C:His100 3.83 Cu CD2 C:His100 3.08 Cu CE1 C:His100 2.59 Cu HD1 C:His100 4.64 Cu CG C:His100 4.08 Cu NE2 C:His135 2.14 Cu ND1 C:His135 4.26 Cu CD2 C:His135 3.19 Cu CE1 C:His135 3.10 Cu CG C:His135 4.33 Cu O1 C:No2503 2.40 Cu O2 C:No2503 2.30 Cu N C:No2503 2.58 Cu H1 A:Hoh544 4.23 Cu H2 C:Hoh638 4.33 Cu H2 C:Hoh737 4.38 interactive model: