Zinc in the structure of New Refinement Of the Crystal Structure Of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum (pdb 3lvz)

The binding sites of Zinc atom in the structure of New Refinement Of the Crystal Structure Of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum (pdb code 3lvz). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3lvz structure was solved by J.D.DOCQUIER, M.BENVENUTI, V.CALDERONE, M.STOCZKO, G.M.ROSSOLINI, S.MANGANI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.2-1.4 Space group P1 a (A) 42.501 b (A) 44.773 c (A) 76.966 alpha (°) 78.92 beta (°) 89.51 gamma (°) 61.91 Rfactor (%) 16.2 Rfree (%) 19.3 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His101, A: His103, A: Asp105, A: His106, A: His177, A: Zn296, A: Hoh299, A: Hoh302, A: Hoh382, A: Hoh444, conact list: Atom Atom Distance (A) Zn NE2 A:His101 2.06 Zn ND1 A:His101 4.10 Zn CD2 A:His101 2.99 Zn CE1 A:His101 3.00 Zn CG A:His101 4.11 Zn NE2 A:His103 4.15 Zn CB A:His103 3.53 Zn ND1 A:His103 2.08 Zn CD2 A:His103 4.23 Zn CE1 A:His103 3.02 Zn CG A:His103 3.14 Zn CA A:His103 4.92 Zn OD2 A:Asp105 4.68 Zn OD1 A:Asp105 4.08 Zn CG A:Asp105 4.86 Zn NE2 A:His106 4.17 Zn CD2 A:His106 4.15 Zn NE2 A:His177 2.03 Zn ND1 A:His177 4.17 Zn CD2 A:His177 2.95 Zn CE1 A:His177 3.09 Zn CG A:His177 4.14 Zn ZN A:Zn296 3.45 Zn O A:Hoh299 3.26 Zn O A:Hoh302 1.94 Zn O A:Hoh382 4.61 Zn O A:Hoh444 3.29 interactive model: Zinc binding site 2 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Trp34, A: His101, A: Asp105, A: His106, A: His177, A: His242, A: Zn295, A: Hoh299, A: Hoh302, A: Hoh444, conact list: Atom Atom Distance (A) Zn CZ2 A:Trp34 4.75 Zn CH2 A:Trp34 4.64 Zn NE2 A:His101 3.99 Zn CE1 A:His101 4.06 Zn CB A:Asp105 4.32 Zn OD2 A:Asp105 2.06 Zn OD1 A:Asp105 3.29 Zn CG A:Asp105 3.04 Zn NE2 A:His106 2.07 Zn ND1 A:His106 4.09 Zn CD2 A:His106 3.09 Zn CE1 A:His106 2.96 Zn CG A:His106 4.19 Zn NE2 A:His177 4.80 Zn NE2 A:His242 2.05 Zn ND1 A:His242 4.14 Zn CD2 A:His242 3.06 Zn CE1 A:His242 3.01 Zn CG A:His242 4.17 Zn ZN A:Zn295 3.45 Zn O A:Hoh299 2.53 Zn O A:Hoh302 2.06 Zn O A:Hoh444 4.05 interactive model: Zinc binding site 3 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu158, A: Ala171, A: His172, A: Ala173, A: Lys229, A: Met233, A: Hoh429, conact list: Atom Atom Distance (A) Zn OE1 A:Glu158 2.86 Zn OE2 A:Glu158 1.99 Zn CD A:Glu158 2.81 Zn CG A:Glu158 4.20 Zn O A:Ala171 4.91 Zn NE2 A:His172 4.08 Zn CB A:His172 3.60 Zn ND1 A:His172 2.07 Zn CD2 A:His172 4.23 Zn C A:His172 4.96 Zn CE1 A:His172 2.90 Zn CG A:His172 3.18 Zn CA A:His172 4.11 Zn N A:Ala173 4.94 Zn CE A:Lys229 3.15 Zn CD A:Lys229 4.50 Zn NZ A:Lys229 2.02 Zn CE A:Met233 3.99 Zn O A:Hoh429 4.20 interactive model: Zinc binding site 4 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Trp34, B: His101, B: Asp105, B: His106, B: His177, B: His242, B: Zn296, B: Hoh298, B: Hoh393, B: Hoh482, conact list: Atom Atom Distance (A) Zn CZ3 B:Trp34 4.69 Zn CH2 B:Trp34 4.31 Zn NE2 B:His101 3.96 Zn CE1 B:His101 4.05 Zn CB B:Asp105 4.35 Zn OD2 B:Asp105 2.09 Zn OD1 B:Asp105 3.31 Zn CG B:Asp105 3.08 Zn NE2 B:His106 2.09 Zn ND1 B:His106 4.11 Zn CD2 B:His106 3.15 Zn CE1 B:His106 2.95 Zn CG B:His106 4.23 Zn NE2 B:His177 4.72 Zn NE2 B:His242 2.08 Zn ND1 B:His242 4.16 Zn CD2 B:His242 3.10 Zn CE1 B:His242 3.04 Zn CG B:His242 4.21 Zn ZN B:Zn296 3.43 Zn O B:Hoh298 2.45 Zn O B:Hoh393 4.09 Zn O B:Hoh482 1.96 interactive model: Zinc binding site 5 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His101, B: His103, B: Asp105, B: His106, B: His177, B: Zn295, B: Hoh298, B: Hoh381, B: Hoh393, B: Hoh482, conact list: Atom Atom Distance (A) Zn NE2 B:His101 2.07 Zn ND1 B:His101 4.10 Zn CD2 B:His101 2.99 Zn CE1 B:His101 3.05 Zn CG B:His101 4.10 Zn NE2 B:His103 4.17 Zn CB B:His103 3.53 Zn ND1 B:His103 2.11 Zn CD2 B:His103 4.24 Zn CE1 B:His103 3.04 Zn CG B:His103 3.15 Zn CA B:His103 4.91 Zn OD2 B:Asp105 4.69 Zn OD1 B:Asp105 4.13 Zn CG B:Asp105 4.92 Zn NE2 B:His106 4.16 Zn CD2 B:His106 4.21 Zn NE2 B:His177 1.97 Zn ND1 B:His177 4.10 Zn CD2 B:His177 2.89 Zn CE1 B:His177 3.04 Zn CG B:His177 4.08 Zn ZN B:Zn295 3.43 Zn O B:Hoh298 3.23 Zn O B:Hoh381 4.63 Zn O B:Hoh393 3.21 Zn O B:Hoh482 1.99 interactive model: Zinc binding site 6 out of 6 in 3lvz Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3lvz. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu158, B: Ala171, B: His172, B: Ala173, B: Lys229, B: Met233, conact list: Atom Atom Distance (A) Zn OE1 B:Glu158 2.86 Zn OE2 B:Glu158 1.95 Zn CD B:Glu158 2.77 Zn CG B:Glu158 4.20 Zn O B:Ala171 4.98 Zn NE2 B:His172 4.16 Zn CB B:His172 3.59 Zn ND1 B:His172 2.11 Zn CD2 B:His172 4.27 Zn C B:His172 4.95 Zn CE1 B:His172 2.98 Zn CG B:His172 3.20 Zn CA B:His172 4.10 Zn N B:Ala173 4.98 Zn CE B:Lys229 3.10 Zn CD B:Lys229 4.45 Zn CG B:Lys229 4.98 Zn NZ B:Lys229 2.04 Zn CE B:Met233 4.30 interactive model: