Copper in the structure of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis (pdb 2b08)

The binding sites of Copper atom in the structure of Reduced Acetamide-Bound M150G Nitrite Reductase From Alcaligenes Faecalis (pdb code 2b08). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2b08 structure was solved by H.J.WIJMA, I.S.MACPHERSON, O.FARVER, E.I.TOCHEVA, I.PECHT, M.PH.VERBEET, M.E.P.MURPHY, G.W.CANTERS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 84.5-1.9 Space group P212121 a (A) 60.972 b (A) 102.047 c (A) 146.423 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.7 Rfree (%) 22 Copper Binding Sites: Copper binding site 1 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2b08. 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: Acm1503, conact list: Atom Atom Distance (A) Cu CB A:Met62 4.16 Cu CE A:Met62 3.01 Cu CG A:Met62 3.18 Cu SD A:Met62 2.29 Cu O A:Met94 4.45 Cu NE2 A:His95 4.23 Cu CB A:His95 3.61 Cu ND1 A:His95 2.18 Cu CD2 A:His95 4.33 Cu CE1 A:His95 3.08 Cu CG A:His95 3.24 Cu CA A:His95 4.09 Cu N A:Asn96 4.98 Cu CB A:Cys136 3.24 Cu SG A:Cys136 2.27 Cu CA A:Cys136 4.68 Cu CD A:Pro138 4.73 Cu CG A:Pro138 4.40 Cu NE2 A:His145 4.15 Cu CB A:His145 3.63 Cu ND1 A:His145 2.12 Cu CD2 A:His145 4.27 Cu CE1 A:His145 2.99 Cu CG A:His145 3.21 Cu CA A:His145 4.71 Cu O A:Acm1503 4.79 Cu C2 A:Acm1503 4.89 interactive model: Copper binding site 2 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2b08. 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: Hoh1808, conact list: Atom Atom Distance (A) Cu OD2 A:Asp98 4.80 Cu OD1 A:Asp98 3.67 Cu CG A:Asp98 4.36 Cu NE2 A:His100 2.07 Cu ND1 A:His100 4.12 Cu CD2 A:His100 3.16 Cu CE1 A:His100 2.95 Cu CG A:His100 4.24 Cu NE2 A:His135 2.00 Cu ND1 A:His135 4.12 Cu CD2 A:His135 2.87 Cu CE1 A:His135 3.08 Cu CG A:His135 4.06 Cu NE2 B:His255 4.22 Cu ND1 B:His255 4.75 Cu CD2 B:His255 4.67 Cu CE1 B:His255 4.33 Cu CG B:His255 4.99 Cu NE2 B:His306 2.04 Cu ND1 B:His306 4.06 Cu CD2 B:His306 3.16 Cu CE1 B:His306 2.89 Cu CG B:His306 4.22 Cu CD2 B:Leu308 4.83 Cu O A:Hoh1808 4.40 interactive model: Copper binding site 3 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2b08. 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: Leu93, A: Met94, A: Pro138, A: Met141, A: Trp144, A: His145, A: Hoh1542, A: Hoh1655, conact list: Atom Atom Distance (A) Cu CB A:Leu93 4.57 Cu CD1 A:Leu93 4.61 Cu CD2 A:Leu93 4.35 Cu CG A:Leu93 4.75 Cu O A:Met94 4.30 Cu CB A:Pro138 4.23 Cu CG A:Pro138 4.10 Cu O A:Met141 4.89 Cu CB A:Met141 3.53 Cu CE A:Met141 2.85 Cu CG A:Met141 3.80 Cu SD A:Met141 2.73 Cu CA A:Met141 4.98 Cu CE3 A:Trp144 4.06 Cu CZ3 A:Trp144 3.92 Cu NE2 A:His145 2.04 Cu ND1 A:His145 4.12 Cu CD2 A:His145 2.96 Cu CE1 A:His145 3.05 Cu CG A:His145 4.11 Cu O A:Hoh1542 4.29 Cu O A:Hoh1655 2.02 interactive model: Copper binding site 4 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2b08. 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: Cu12505, B: Acm2503, conact list: Atom Atom Distance (A) Cu CB B:Met62 4.25 Cu CE B:Met62 3.17 Cu CG B:Met62 3.18 Cu SD B:Met62 2.24 Cu O B:Met94 4.42 Cu NE2 B:His95 4.22 Cu CB B:His95 3.48 Cu ND1 B:His95 2.15 Cu CD2 B:His95 4.28 Cu CE1 B:His95 3.09 Cu CG B:His95 3.16 Cu CA B:His95 4.04 Cu N B:Asn96 4.89 Cu CB B:Cys136 3.15 Cu SG B:Cys136 2.27 Cu CA B:Cys136 4.57 Cu CD B:Pro138 4.83 Cu CG B:Pro138 4.49 Cu NE2 B:His145 4.50 Cu CB B:His145 3.78 Cu ND1 B:His145 2.45 Cu CD2 B:His145 4.59 Cu CE1 B:His145 3.34 Cu CG B:His145 3.48 Cu CA B:His145 4.89 Cu CU B:Cu12505 2.12 Cu O B:Acm2503 3.75 Cu C1 B:Acm2503 4.97 interactive model: Copper binding site 5 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2b08. 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: Ile257, C: His306, C: Leu308, B: Hoh2649, B: Hoh2709, conact list: Atom Atom Distance (A) Cu OD2 B:Asp98 4.82 Cu OD1 B:Asp98 3.78 Cu CG B:Asp98 4.34 Cu NE2 B:His100 2.02 Cu ND1 B:His100 4.02 Cu CD2 B:His100 3.16 Cu CE1 B:His100 2.84 Cu CG B:His100 4.20 Cu NE2 B:His135 2.01 Cu ND1 B:His135 4.15 Cu CD2 B:His135 2.87 Cu CE1 B:His135 3.11 Cu CG B:His135 4.07 Cu NE2 C:His255 4.23 Cu ND1 C:His255 4.83 Cu CD2 C:His255 4.62 Cu CE1 C:His255 4.40 Cu CG C:His255 4.97 Cu CG1 C:Ile257 5.00 Cu NE2 C:His306 2.08 Cu ND1 C:His306 4.15 Cu CD2 C:His306 3.09 Cu CE1 C:His306 3.03 Cu CG C:His306 4.21 Cu CD2 C:Leu308 4.90 Cu O B:Hoh2649 4.63 Cu O B:Hoh2709 4.99 interactive model: Copper binding site 6 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2b08. 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: Ala137, B: Pro138, B: His145, B: Cu12501, B: Acm2503, B: Hoh2648, conact list: Atom Atom Distance (A) Cu SD B:Met62 4.10 Cu O B:Met94 3.90 Cu C B:Met94 4.81 Cu N B:His95 4.92 Cu CB B:His95 4.24 Cu ND1 B:His95 3.56 Cu C B:His95 4.82 Cu CE1 B:His95 4.51 Cu CG B:His95 4.30 Cu CA B:His95 3.99 Cu N B:Asn96 4.55 Cu OD1 B:Asn96 4.44 Cu O B:Cys136 4.96 Cu CB B:Cys136 3.26 Cu SG B:Cys136 2.03 Cu C B:Cys136 4.32 Cu CA B:Cys136 4.28 Cu N B:Ala137 4.29 Cu C B:Ala137 4.91 Cu CA B:Ala137 4.94 Cu N B:Pro138 3.99 Cu CB B:Pro138 3.85 Cu CD B:Pro138 2.76 Cu CG B:Pro138 2.42 Cu CA B:Pro138 4.65 Cu NE2 B:His145 3.56 Cu CB B:His145 3.18 Cu ND1 B:His145 2.02 Cu CD2 B:His145 3.53 Cu CE1 B:His145 2.77 Cu CG B:His145 2.66 Cu CA B:His145 4.65 Cu CU B:Cu12501 2.12 Cu O B:Acm2503 4.69 Cu O B:Hoh2648 4.91 interactive model: Copper binding site 7 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 2b08. 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: Cu13505, conact list: Atom Atom Distance (A) Cu CB C:Met62 4.31 Cu CE C:Met62 3.29 Cu CG C:Met62 3.23 Cu SD C:Met62 2.12 Cu O C:Met94 4.33 Cu NE2 C:His95 4.32 Cu N C:His95 4.99 Cu CB C:His95 3.62 Cu ND1 C:His95 2.26 Cu CD2 C:His95 4.40 Cu CE1 C:His95 3.17 Cu CG C:His95 3.29 Cu CA C:His95 4.01 Cu N C:Asn96 4.91 Cu CB C:Cys136 3.27 Cu SG C:Cys136 2.33 Cu CA C:Cys136 4.70 Cu CD C:Pro138 4.84 Cu CG C:Pro138 4.58 Cu NE2 C:His145 4.32 Cu CB C:His145 3.69 Cu ND1 C:His145 2.28 Cu CD2 C:His145 4.43 Cu CE1 C:His145 3.16 Cu CG C:His145 3.33 Cu CA C:His145 4.81 Cu CU C:Cu13505 1.93 interactive model: Copper binding site 8 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 2b08. 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: Ile257, A: His306, C: Asp98, C: His100, C: His135, A: Hoh1543, C: Hoh3636, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.20 Cu ND1 A:His255 4.71 Cu CD2 A:His255 4.59 Cu CE1 A:His255 4.30 Cu CG A:His255 4.90 Cu CG1 A:Ile257 4.80 Cu NE2 A:His306 2.14 Cu ND1 A:His306 4.13 Cu CD2 A:His306 3.23 Cu CE1 A:His306 2.96 Cu CG A:His306 4.28 Cu OD2 C:Asp98 4.73 Cu OD1 C:Asp98 3.75 Cu CG C:Asp98 4.30 Cu NE2 C:His100 2.05 Cu ND1 C:His100 4.12 Cu CD2 C:His100 3.10 Cu CE1 C:His100 2.98 Cu CG C:His100 4.21 Cu NE2 C:His135 2.12 Cu ND1 C:His135 4.26 Cu CD2 C:His135 2.88 Cu CE1 C:His135 3.26 Cu CG C:His135 4.12 Cu O A:Hoh1543 4.96 Cu O C:Hoh3636 4.46 interactive model: Copper binding site 9 out of 9 in 2b08 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Copper in the PDB 2b08. 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: Ala137, C: Pro138, C: His145, C: Cu13501, conact list: Atom Atom Distance (A) Cu CE C:Met62 4.87 Cu SD C:Met62 3.82 Cu O C:Met94 3.80 Cu C C:Met94 4.69 Cu N C:His95 4.77 Cu CB C:His95 4.20 Cu ND1 C:His95 3.56 Cu C C:His95 4.68 Cu CE1 C:His95 4.52 Cu CG C:His95 4.27 Cu CA C:His95 3.85 Cu N C:Asn96 4.42 Cu OD1 C:Asn96 4.42 Cu CB C:Cys136 3.23 Cu SG C:Cys136 1.96 Cu C C:Cys136 4.38 Cu CA C:Cys136 4.30 Cu N C:Ala137 4.26 Cu C C:Ala137 4.95 Cu N C:Pro138 4.06 Cu CB C:Pro138 3.89 Cu CD C:Pro138 2.96 Cu CG C:Pro138 2.71 Cu CA C:Pro138 4.70 Cu NE2 C:His145 3.64 Cu CB C:His145 3.22 Cu ND1 C:His145 2.04 Cu CD2 C:His145 3.62 Cu CE1 C:His145 2.81 Cu CG C:His145 2.72 Cu CA C:His145 4.68 Cu CU C:Cu13501 1.93 interactive model: