Copper in the structure of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 (pdb 1rkr)

The binding sites of Copper atom in the structure of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 (pdb code 1rkr). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 1rkr structure was solved by C.LI, T.INOUE, M.GOTOWDA, S.SUZUKI, K.YAMAGUCHI, K.KATAOKA, Y.KAI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.5 Space group C121 a (A) 130.670 b (A) 54.260 c (A) 74.550 alpha (°) 90.00 beta (°) 95.99 gamma (°) 90.00 Rfactor (%) 17.3 Rfree (%) 23.6 Copper Binding Sites: Copper binding site 1 out of 4 in 1rkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 1rkr. 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: Gly45, A: His46, A: Asn47, A: Cys112, A: Phe114, A: His117, A: Met121, conact list: Atom Atom Distance (A) Cu O A:Gly45 2.51 Cu C A:Gly45 3.62 Cu CA A:Gly45 4.94 Cu NE2 A:His46 4.11 Cu N A:His46 3.98 Cu CB A:His46 3.57 Cu ND1 A:His46 2.02 Cu CD2 A:His46 4.22 Cu C A:His46 4.61 Cu CE1 A:His46 2.96 Cu CG A:His46 3.08 Cu CA A:His46 3.42 Cu N A:Asn47 4.65 Cu CB A:Cys112 3.42 Cu SG A:Cys112 2.14 Cu CA A:Cys112 4.77 Cu N A:Phe114 4.94 Cu CB A:Phe114 3.70 Cu CD1 A:Phe114 4.72 Cu CG A:Phe114 4.38 Cu CA A:Phe114 4.90 Cu NE2 A:His117 3.95 Cu CB A:His117 3.48 Cu ND1 A:His117 1.93 Cu CD2 A:His117 4.13 Cu CE1 A:His117 2.78 Cu CG A:His117 3.03 Cu CA A:His117 4.95 Cu CE A:Met121 4.32 Cu CG A:Met121 4.64 Cu SD A:Met121 3.14 interactive model: Copper binding site 2 out of 4 in 1rkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 1rkr. 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: Gly45, B: His46, B: Asn47, B: Cys112, B: Phe114, B: His117, B: Met121, conact list: Atom Atom Distance (A) Cu O B:Gly45 2.46 Cu C B:Gly45 3.53 Cu CA B:Gly45 4.87 Cu NE2 B:His46 4.02 Cu N B:His46 3.87 Cu CB B:His46 3.54 Cu ND1 B:His46 1.96 Cu CD2 B:His46 4.15 Cu C B:His46 4.51 Cu CE1 B:His46 2.87 Cu CG B:His46 3.03 Cu CA B:His46 3.32 Cu N B:Asn47 4.57 Cu CB B:Cys112 3.50 Cu SG B:Cys112 2.14 Cu CA B:Cys112 4.82 Cu O B:Phe114 4.93 Cu N B:Phe114 4.90 Cu CB B:Phe114 3.89 Cu CD1 B:Phe114 4.98 Cu CG B:Phe114 4.62 Cu CA B:Phe114 4.98 Cu NE2 B:His117 4.06 Cu CB B:His117 3.43 Cu ND1 B:His117 1.99 Cu CD2 B:His117 4.18 Cu CE1 B:His117 2.92 Cu CG B:His117 3.03 Cu CA B:His117 4.91 Cu CE B:Met121 4.22 Cu CG B:Met121 4.67 Cu SD B:Met121 3.21 interactive model: Copper binding site 3 out of 4 in 1rkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 1rkr. 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: Gly45, C: His46, C: Asn47, C: Cys112, C: Phe114, C: His117, C: Met121, conact list: Atom Atom Distance (A) Cu O C:Gly45 2.49 Cu C C:Gly45 3.56 Cu CA C:Gly45 4.90 Cu NE2 C:His46 3.93 Cu N C:His46 3.89 Cu CB C:His46 3.44 Cu ND1 C:His46 1.88 Cu CD2 C:His46 4.06 Cu C C:His46 4.59 Cu CE1 C:His46 2.79 Cu CG C:His46 2.94 Cu CA C:His46 3.33 Cu N C:Asn47 4.60 Cu CB C:Cys112 3.47 Cu SG C:Cys112 2.24 Cu CA C:Cys112 4.82 Cu N C:Phe114 4.96 Cu CB C:Phe114 3.86 Cu CD1 C:Phe114 4.96 Cu CG C:Phe114 4.61 Cu NE2 C:His117 3.94 Cu CB C:His117 3.41 Cu ND1 C:His117 1.87 Cu CD2 C:His117 4.08 Cu CE1 C:His117 2.77 Cu CG C:His117 2.94 Cu CA C:His117 4.90 Cu CE C:Met121 4.05 Cu CG C:Met121 4.61 Cu SD C:Met121 3.14 interactive model: Copper binding site 4 out of 4 in 1rkr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 1rkr. 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: D: Gly45, D: His46, D: Asn47, D: Cys112, D: Phe114, D: His117, D: Met121, conact list: Atom Atom Distance (A) Cu O D:Gly45 2.59 Cu C D:Gly45 3.65 Cu NE2 D:His46 4.10 Cu N D:His46 3.91 Cu CB D:His46 3.45 Cu ND1 D:His46 2.03 Cu CD2 D:His46 4.19 Cu C D:His46 4.41 Cu CE1 D:His46 2.99 Cu CG D:His46 3.04 Cu CA D:His46 3.26 Cu N D:Asn47 4.42 Cu CB D:Cys112 3.42 Cu SG D:Cys112 2.12 Cu CA D:Cys112 4.73 Cu N D:Phe114 4.93 Cu CB D:Phe114 3.90 Cu CD1 D:Phe114 4.92 Cu CG D:Phe114 4.60 Cu NE2 D:His117 4.10 Cu CB D:His117 3.51 Cu ND1 D:His117 1.91 Cu CD2 D:His117 4.11 Cu CE1 D:His117 2.86 Cu CG D:His117 2.97 Cu CE D:Met121 4.11 Cu CG D:Met121 4.72 Cu SD D:Met121 3.24 interactive model: