Copper in the structure of Crystal Structure Of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis (pdb 1npn)

The binding sites of Copper atom in the structure of Crystal Structure Of A Copper Reconstituted H145A Mutant of Nitrite Reductase From Alcaligenes Faecalis (pdb code 1npn). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1npn structure was solved by H.J.WIJMA, M.J.BOULANGER, A.MOLON, M.FITTIPALDI, M.HUBER, M.E.MURPHY, M.P.VERBEET, G.W.CANTERS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 33.3-1.8 Space group P212121 a (A) 61.600 b (A) 102.520 c (A) 146.070 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.6 Rfree (%) 19.5 Copper Binding Sites: Copper binding site 1 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1npn. 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: Ala145, A: Met150, A: Cl498, A: Hoh5498, conact list: Atom Atom Distance (A) Cu CB A:Met62 4.74 Cu O A:Met94 4.19 Cu C A:Met94 4.93 Cu NE2 A:His95 4.07 Cu N A:His95 4.84 Cu CB A:His95 3.49 Cu ND1 A:His95 2.03 Cu CD2 A:His95 4.17 Cu C A:His95 4.80 Cu CE1 A:His95 2.93 Cu CG A:His95 3.09 Cu CA A:His95 3.80 Cu N A:Asn96 4.62 Cu CB A:Cys136 3.15 Cu SG A:Cys136 2.19 Cu CA A:Cys136 4.58 Cu CD A:Pro138 4.69 Cu CG A:Pro138 4.77 Cu CB A:Ala145 4.15 Cu CB A:Met150 4.44 Cu CE A:Met150 3.43 Cu CG A:Met150 4.03 Cu SD A:Met150 2.66 Cu CL A:Cl498 2.31 Cu O A:Hoh5498 4.29 interactive model: Copper binding site 2 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1npn. 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: Hoh5497, B: Hoh503, B: Hoh1097, conact list: Atom Atom Distance (A) Cu OD2 A:Asp98 3.71 Cu OD1 A:Asp98 4.82 Cu CG A:Asp98 4.42 Cu NE2 A:His100 2.02 Cu ND1 A:His100 4.06 Cu CD2 A:His100 3.11 Cu CE1 A:His100 2.90 Cu CG A:His100 4.19 Cu NE2 A:His135 2.10 Cu ND1 A:His135 4.21 Cu CD2 A:His135 3.03 Cu CE1 A:His135 3.13 Cu CG A:His135 4.20 Cu NE2 B:His255 4.24 Cu ND1 B:His255 4.66 Cu CD2 B:His255 4.67 Cu CE1 B:His255 4.25 Cu CG B:His255 4.93 Cu NE2 B:His306 2.09 Cu ND1 B:His306 4.12 Cu CD2 B:His306 3.18 Cu CE1 B:His306 2.95 Cu CG B:His306 4.26 Cu CD1 B:Leu308 4.92 Cu CD2 B:Leu308 4.94 Cu O A:Hoh5497 4.22 Cu O B:Hoh503 2.21 Cu O B:Hoh1097 4.95 interactive model: Copper binding site 3 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1npn. 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: Ala145, B: Met150, B: Cl499, conact list: Atom Atom Distance (A) Cu CB B:Met62 4.71 Cu CE B:Met62 4.69 Cu O B:Met94 4.25 Cu C B:Met94 4.95 Cu NE2 B:His95 4.07 Cu N B:His95 4.82 Cu CB B:His95 3.39 Cu ND1 B:His95 2.01 Cu CD2 B:His95 4.13 Cu C B:His95 4.77 Cu CE1 B:His95 2.95 Cu CG B:His95 3.02 Cu CA B:His95 3.77 Cu N B:Asn96 4.62 Cu CB B:Cys136 3.16 Cu SG B:Cys136 2.20 Cu CA B:Cys136 4.60 Cu CD B:Pro138 4.82 Cu CG B:Pro138 4.20 Cu CB B:Ala145 4.27 Cu CB B:Met150 4.48 Cu CE B:Met150 3.25 Cu CG B:Met150 4.03 Cu SD B:Met150 2.62 Cu CL B:Cl499 2.41 interactive model: Copper binding site 4 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1npn. 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, B: Hoh5489, C: Hoh504, conact list: Atom Atom Distance (A) Cu OD2 B:Asp98 3.72 Cu OD1 B:Asp98 4.85 Cu CG B:Asp98 4.40 Cu NE2 B:His100 2.07 Cu ND1 B:His100 4.13 Cu CD2 B:His100 3.12 Cu CE1 B:His100 3.00 Cu CG B:His100 4.23 Cu NE2 B:His135 2.04 Cu ND1 B:His135 4.16 Cu CD2 B:His135 2.94 Cu CE1 B:His135 3.10 Cu CG B:His135 4.12 Cu NE2 C:His255 4.29 Cu ND1 C:His255 4.54 Cu CD2 C:His255 4.73 Cu CE1 C:His255 4.18 Cu CG C:His255 4.89 Cu NE2 C:His306 2.10 Cu ND1 C:His306 4.19 Cu CD2 C:His306 3.12 Cu CE1 C:His306 3.05 Cu CG C:His306 4.26 Cu CD1 C:Leu308 4.87 Cu CD2 C:Leu308 4.97 Cu O B:Hoh5489 4.43 Cu O C:Hoh504 2.23 interactive model: Copper binding site 5 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 1npn. 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: Ala145, C: Met150, C: Cl500, conact list: Atom Atom Distance (A) Cu CB C:Met62 4.63 Cu CG C:Met62 5.00 Cu O C:Met94 4.20 Cu C C:Met94 4.91 Cu NE2 C:His95 4.13 Cu N C:His95 4.78 Cu CB C:His95 3.40 Cu ND1 C:His95 2.07 Cu CD2 C:His95 4.17 Cu C C:His95 4.75 Cu CE1 C:His95 3.02 Cu CG C:His95 3.06 Cu CA C:His95 3.74 Cu N C:Asn96 4.60 Cu CB C:Cys136 3.12 Cu SG C:Cys136 2.19 Cu CA C:Cys136 4.55 Cu CD C:Pro138 4.64 Cu CG C:Pro138 4.55 Cu CB C:Ala145 4.16 Cu CB C:Met150 4.50 Cu CE C:Met150 3.37 Cu CG C:Met150 4.04 Cu SD C:Met150 2.71 Cu CL C:Cl500 2.16 interactive model: Copper binding site 6 out of 6 in 1npn Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 1npn. 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, A: Leu308, C: Asp98, C: His100, C: His135, A: Hoh505, C: Hoh5488, conact list: Atom Atom Distance (A) Cu NE2 A:His255 4.26 Cu ND1 A:His255 4.49 Cu CD2 A:His255 4.75 Cu CE1 A:His255 4.11 Cu CG A:His255 4.89 Cu CD1 A:Ile257 4.47 Cu NE2 A:His306 2.10 Cu ND1 A:His306 4.16 Cu CD2 A:His306 3.15 Cu CE1 A:His306 3.01 Cu CG A:His306 4.26 Cu CD1 A:Leu308 4.86 Cu CD2 A:Leu308 4.98 Cu OD2 C:Asp98 3.70 Cu OD1 C:Asp98 4.83 Cu CG C:Asp98 4.44 Cu NE2 C:His100 2.03 Cu ND1 C:His100 4.04 Cu CD2 C:His100 3.15 Cu CE1 C:His100 2.86 Cu CG C:His100 4.20 Cu NE2 C:His135 2.13 Cu ND1 C:His135 4.25 Cu CD2 C:His135 3.00 Cu CE1 C:His135 3.20 Cu CG C:His135 4.19 Cu O A:Hoh505 2.20 Cu O C:Hoh5488 4.28 interactive model: