Copper in the structure of Crystal Structure Analysis of Oxidized Pseudomonas Aeruginosa Azurin At pH 5.5 and pH 9.0. A pH-Induced Conformational Transition Involves A Peptide Bond Flip (pdb 5azu)

The binding sites of Copper atom in the structure of Crystal Structure Analysis of Oxidized Pseudomonas Aeruginosa Azurin At pH 5.5 and pH 9.0. A pH-Induced Conformational Transition Involves A Peptide Bond Flip (pdb code 5azu). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 5azu structure was solved by H.NAR, A.MESSERSCHMIDT, R.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 1.9 Space group P212121 a (A) 57.760 b (A) 81.090 c (A) 109.940 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) n/a Rfree (%) n/a Copper Binding Sites: Copper binding site 1 out of 4 in 5azu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 5azu. 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 2.83 Cu C A:Gly45 3.77 Cu NE2 A:His46 4.06 Cu N A:His46 4.01 Cu CB A:His46 3.52 Cu ND1 A:His46 1.98 Cu CD2 A:His46 4.18 Cu C A:His46 4.57 Cu CE1 A:His46 2.92 Cu CG A:His46 3.04 Cu CA A:His46 3.37 Cu N A:Asn47 4.68 Cu CB A:Cys112 3.34 Cu SG A:Cys112 2.28 Cu CA A:Cys112 4.75 Cu N A:Phe114 4.85 Cu CB A:Phe114 3.86 Cu CG A:Phe114 4.72 Cu CA A:Phe114 4.97 Cu NE2 A:His117 4.13 Cu CB A:His117 3.42 Cu ND1 A:His117 2.06 Cu CD2 A:His117 4.23 Cu CE1 A:His117 3.01 Cu CG A:His117 3.07 Cu CA A:His117 4.94 Cu CB A:Met121 5.00 Cu CE A:Met121 3.99 Cu CG A:Met121 4.67 Cu SD A:Met121 3.15 interactive model: Copper binding site 2 out of 4 in 5azu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 5azu. 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 2.87 Cu C B:Gly45 3.82 Cu NE2 B:His46 4.14 Cu N B:His46 4.05 Cu CB B:His46 3.54 Cu ND1 B:His46 2.08 Cu CD2 B:His46 4.25 Cu C B:His46 4.53 Cu CE1 B:His46 3.02 Cu CG B:His46 3.10 Cu CA B:His46 3.37 Cu N B:Asn47 4.62 Cu CB B:Cys112 3.30 Cu SG B:Cys112 2.29 Cu CA B:Cys112 4.69 Cu N B:Phe114 4.82 Cu CB B:Phe114 3.84 Cu CG B:Phe114 4.65 Cu CA B:Phe114 4.94 Cu NE2 B:His117 4.14 Cu CB B:His117 3.51 Cu ND1 B:His117 2.08 Cu CD2 B:His117 4.26 Cu CE1 B:His117 3.01 Cu CG B:His117 3.11 Cu CB B:Met121 4.96 Cu CE B:Met121 3.92 Cu CG B:Met121 4.62 Cu SD B:Met121 3.11 interactive model: Copper binding site 3 out of 4 in 5azu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 5azu. 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 2.98 Cu C C:Gly45 3.88 Cu NE2 C:His46 4.22 Cu N C:His46 4.05 Cu CB C:His46 3.46 Cu ND1 C:His46 2.12 Cu CD2 C:His46 4.28 Cu C C:His46 4.51 Cu CE1 C:His46 3.11 Cu CG C:His46 3.11 Cu CA C:His46 3.33 Cu N C:Asn47 4.62 Cu CB C:Cys112 3.24 Cu SG C:Cys112 2.20 Cu CA C:Cys112 4.66 Cu N C:Phe114 4.89 Cu CB C:Phe114 3.91 Cu CG C:Phe114 4.75 Cu NE2 C:His117 4.08 Cu CB C:His117 3.38 Cu ND1 C:His117 2.00 Cu CD2 C:His117 4.20 Cu CE1 C:His117 2.95 Cu CG C:His117 3.03 Cu CA C:His117 4.88 Cu CE C:Met121 3.85 Cu CG C:Met121 4.74 Cu SD C:Met121 3.19 interactive model: Copper binding site 4 out of 4 in 5azu Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 5azu. 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 3.02 Cu C D:Gly45 3.91 Cu NE2 D:His46 4.16 Cu N D:His46 4.08 Cu CB D:His46 3.48 Cu ND1 D:His46 2.07 Cu CD2 D:His46 4.25 Cu C D:His46 4.57 Cu CE1 D:His46 3.04 Cu CG D:His46 3.08 Cu CA D:His46 3.39 Cu N D:Asn47 4.63 Cu CB D:Cys112 3.32 Cu SG D:Cys112 2.25 Cu CA D:Cys112 4.68 Cu N D:Phe114 4.81 Cu CB D:Phe114 3.91 Cu CG D:Phe114 4.82 Cu CA D:Phe114 4.97 Cu NE2 D:His117 4.08 Cu CB D:His117 3.35 Cu ND1 D:His117 1.99 Cu CD2 D:His117 4.15 Cu CE1 D:His117 2.96 Cu CG D:His117 2.99 Cu CA D:His117 4.87 Cu CB D:Met121 4.92 Cu CE D:Met121 3.92 Cu CG D:Met121 4.58 Cu SD D:Met121 3.08 interactive model: