Copper in the structure of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb 1ndt)

The binding sites of Copper atom in the structure of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 1ndt). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1ndt structure was solved by F.E.DODD, J.VANBEEUMEN, R.R.EADY, S.S.HASNAIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.1 Space group P63 a (A) 81.236 b (A) 81.236 c (A) 100.034 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16.7 Rfree (%) 20.8 Copper Binding Sites: Copper binding site 1 out of 2 in 1ndt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1ndt. 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: Met56, A: Pro88, A: His89, A: Asn90, A: Cys130, A: Pro132, A: His139, A: Met144, conact list: Atom Atom Distance (A) Cu SD A:Met56 4.55 Cu O A:Pro88 4.09 Cu C A:Pro88 4.90 Cu NE2 A:His89 4.09 Cu N A:His89 4.84 Cu CB A:His89 3.56 Cu ND1 A:His89 2.06 Cu CD2 A:His89 4.23 Cu C A:His89 4.90 Cu CE1 A:His89 2.93 Cu CG A:His89 3.14 Cu CA A:His89 3.85 Cu N A:Asn90 4.82 Cu CB A:Cys130 3.28 Cu SG A:Cys130 2.21 Cu CA A:Cys130 4.70 Cu CD A:Pro132 4.48 Cu CG A:Pro132 4.10 Cu NE2 A:His139 4.01 Cu CB A:His139 3.43 Cu ND1 A:His139 1.93 Cu CD2 A:His139 4.10 Cu CE1 A:His139 2.87 Cu CG A:His139 2.99 Cu CA A:His139 4.70 Cu CB A:Met144 4.68 Cu CE A:Met144 3.50 Cu CG A:Met144 4.14 Cu SD A:Met144 2.64 interactive model: Copper binding site 2 out of 2 in 1ndt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1ndt. 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: Asp92, A: His94, A: His129, A: Cl503, A: Hoh600, conact list: Atom Atom Distance (A) Cu OD2 A:Asp92 3.92 Cu OD1 A:Asp92 4.96 Cu CG A:Asp92 4.63 Cu NE2 A:His94 2.01 Cu ND1 A:His94 4.07 Cu CD2 A:His94 3.09 Cu CE1 A:His94 2.91 Cu CG A:His94 4.18 Cu NE2 A:His129 2.10 Cu ND1 A:His129 4.22 Cu CD2 A:His129 3.06 Cu CE1 A:His129 3.12 Cu CG A:His129 4.22 Cu CL A:Cl503 2.25 Cu O A:Hoh600 4.89 interactive model: