Zinc in the structure of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II) (pdb 3knr)

The binding sites of Zinc atom in the structure of Bacillus Cereus Metallo-Beta-Lactamase CYS221ASP Mutant, 1 Mm Zn(II) (pdb code 3knr). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3knr structure was solved by F.J.MEDRANO MARTIN, J.M.GONZALEZ, A.J.VILA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 23.3-1.7 Space group P1211 a (A) 80.143 b (A) 94.364 c (A) 79.898 alpha (°) 90.00 beta (°) 120.11 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 21 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3knr. 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: His86, A: His88, A: Asp90, A: His149, A: Thr150, A: Asp168, A: Zn229, A: Hoh267, A: Hoh324, A: Hoh539, A: Hoh685, A: Hoh771, A: Hoh772, conact list: Atom Atom Distance (A) Zn NE2 A:His86 2.07 Zn ND1 A:His86 4.11 Zn CD2 A:His86 3.04 Zn CE1 A:His86 3.01 Zn CG A:His86 4.16 Zn NE2 A:His88 3.92 Zn CB A:His88 3.25 Zn ND1 A:His88 1.86 Zn CD2 A:His88 3.96 Zn CE1 A:His88 2.82 Zn CG A:His88 2.88 Zn CA A:His88 4.74 Zn OD2 A:Asp90 4.98 Zn OD1 A:Asp90 4.32 Zn NE2 A:His149 2.02 Zn ND1 A:His149 4.14 Zn CD2 A:His149 2.92 Zn CE1 A:His149 3.08 Zn CG A:His149 4.10 Zn CG2 A:Thr150 4.25 Zn CB A:Asp168 4.40 Zn CB A:Asp168 4.41 Zn OD2 A:Asp168 4.55 Zn OD1 A:Asp168 3.75 Zn OD1 A:Asp168 4.50 Zn CG A:Asp168 4.40 Zn CG A:Asp168 4.29 Zn ZN A:Zn229 4.53 Zn O A:Hoh267 1.98 Zn O A:Hoh324 4.79 Zn O A:Hoh539 4.41 Zn O A:Hoh685 4.41 Zn O A:Hoh771 4.67 Zn O A:Hoh772 2.64 interactive model: Zinc binding site 2 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3knr. 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: Trp59, A: Asp90, A: Arg91, A: His149, A: Asp168, A: His210, A: Zn228, A: Hoh267, A: Hoh318, A: Hoh364, A: Hoh685, A: Hoh771, A: Hoh772, A: Hoh1150, conact list: Atom Atom Distance (A) Zn CH2 A:Trp59 4.84 Zn CB A:Asp90 4.19 Zn OD2 A:Asp90 1.83 Zn OD1 A:Asp90 3.60 Zn CG A:Asp90 3.01 Zn CZ A:Arg91 4.83 Zn NE A:Arg91 4.66 Zn NH2 A:Arg91 4.17 Zn NE2 A:His149 4.89 Zn CB A:Asp168 3.95 Zn CB A:Asp168 3.94 Zn OD2 A:Asp168 2.86 Zn OD2 A:Asp168 1.91 Zn OD1 A:Asp168 2.82 Zn OD1 A:Asp168 2.52 Zn CG A:Asp168 2.88 Zn CG A:Asp168 2.48 Zn CA A:Asp168 4.98 Zn NE2 A:His210 2.10 Zn ND1 A:His210 4.04 Zn CD2 A:His210 3.27 Zn CE1 A:His210 2.83 Zn CG A:His210 4.28 Zn ZN A:Zn228 4.53 Zn O A:Hoh267 2.97 Zn O A:Hoh318 4.87 Zn O A:Hoh364 4.23 Zn O A:Hoh685 4.11 Zn O A:Hoh771 2.24 Zn O A:Hoh772 4.00 Zn O A:Hoh1150 3.90 interactive model: Zinc binding site 3 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3knr. 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: His86, B: His88, B: Asp90, B: His149, B: Thr150, B: Asp168, B: Hoh266, B: Hoh282, B: Hoh385, B: Hoh767, B: Hoh775, conact list: Atom Atom Distance (A) Zn NE2 B:His86 2.10 Zn ND1 B:His86 4.15 Zn CD2 B:His86 3.06 Zn CE1 B:His86 3.06 Zn CG B:His86 4.20 Zn NE2 B:His88 3.93 Zn CB B:His88 3.27 Zn ND1 B:His88 1.84 Zn CD2 B:His88 3.98 Zn CE1 B:His88 2.83 Zn CG B:His88 2.88 Zn CA B:His88 4.71 Zn OD2 B:Asp90 4.92 Zn OD1 B:Asp90 4.16 Zn CG B:Asp90 4.92 Zn NE2 B:His149 1.97 Zn ND1 B:His149 4.10 Zn CD2 B:His149 2.93 Zn CE1 B:His149 3.01 Zn CG B:His149 4.09 Zn CG2 B:Thr150 4.17 Zn CB B:Asp168 4.42 Zn OD1 B:Asp168 3.86 Zn CG B:Asp168 4.41 Zn O B:Hoh266 4.21 Zn O B:Hoh282 2.56 Zn O B:Hoh385 4.77 Zn O B:Hoh767 1.96 Zn O B:Hoh775 4.23 interactive model: Zinc binding site 4 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3knr. 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: C: His86, C: His88, C: Asp90, C: His149, C: Thr150, C: Asp168, C: Zn229, C: Hoh282, C: Hoh300, C: Hoh496, C: Hoh522, C: Hoh546, C: Hoh776, conact list: Atom Atom Distance (A) Zn NE2 C:His86 2.09 Zn ND1 C:His86 4.13 Zn CD2 C:His86 3.08 Zn CE1 C:His86 3.02 Zn CG C:His86 4.19 Zn NE2 C:His88 3.89 Zn CB C:His88 3.26 Zn ND1 C:His88 1.83 Zn CD2 C:His88 3.95 Zn CE1 C:His88 2.78 Zn CG C:His88 2.87 Zn CA C:His88 4.75 Zn OD2 C:Asp90 4.31 Zn OD1 C:Asp90 4.91 Zn NE2 C:His149 2.01 Zn ND1 C:His149 4.13 Zn CD2 C:His149 2.94 Zn CE1 C:His149 3.05 Zn CG C:His149 4.10 Zn CG2 C:Thr150 4.24 Zn CB C:Asp168 4.41 Zn CB C:Asp168 4.45 Zn OD2 C:Asp168 4.50 Zn OD1 C:Asp168 3.71 Zn OD1 C:Asp168 4.47 Zn CG C:Asp168 4.39 Zn CG C:Asp168 4.27 Zn ZN C:Zn229 4.56 Zn O C:Hoh282 4.32 Zn O C:Hoh300 4.78 Zn O C:Hoh496 4.48 Zn O C:Hoh522 1.98 Zn O C:Hoh546 4.63 Zn O C:Hoh776 2.51 interactive model: Zinc binding site 5 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3knr. 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: C: Trp59, C: Asp90, C: Arg91, C: His149, C: Asp168, C: His210, C: Zn228, C: Hoh282, C: Hoh318, C: Hoh404, C: Hoh522, C: Hoh546, C: Hoh776, C: Hoh1146, C: Hoh1152, C: Hoh1154, conact list: Atom Atom Distance (A) Zn CH2 C:Trp59 4.82 Zn CB C:Asp90 4.22 Zn OD2 C:Asp90 3.70 Zn OD1 C:Asp90 1.86 Zn CG C:Asp90 3.07 Zn CZ C:Arg91 4.83 Zn NE C:Arg91 4.63 Zn NH2 C:Arg91 4.21 Zn NE2 C:His149 4.95 Zn CB C:Asp168 3.94 Zn CB C:Asp168 3.97 Zn OD2 C:Asp168 2.78 Zn OD2 C:Asp168 1.86 Zn OD1 C:Asp168 2.78 Zn OD1 C:Asp168 2.65 Zn CG C:Asp168 2.84 Zn CG C:Asp168 2.53 Zn NE2 C:His210 2.12 Zn ND1 C:His210 4.06 Zn CD2 C:His210 3.29 Zn CE1 C:His210 2.84 Zn CG C:His210 4.30 Zn ZN C:Zn228 4.56 Zn O C:Hoh282 4.08 Zn O C:Hoh318 4.12 Zn O C:Hoh404 4.82 Zn O C:Hoh522 3.06 Zn O C:Hoh546 2.19 Zn O C:Hoh776 4.16 Zn O C:Hoh1146 4.43 Zn O C:Hoh1152 3.88 Zn O C:Hoh1154 4.16 interactive model: Zinc binding site 6 out of 6 in 3knr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3knr. 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: D: His86, D: His88, D: Asp90, D: His149, D: Thr150, D: Asp168, D: Hoh230, D: Hoh248, D: Hoh265, D: Hoh463, D: Hoh652, D: Hoh778, conact list: Atom Atom Distance (A) Zn NE2 D:His86 2.11 Zn ND1 D:His86 4.16 Zn CD2 D:His86 3.07 Zn CE1 D:His86 3.07 Zn CG D:His86 4.20 Zn NE2 D:His88 4.04 Zn CB D:His88 3.28 Zn ND1 D:His88 1.95 Zn CD2 D:His88 4.06 Zn CE1 D:His88 2.94 Zn CG D:His88 2.94 Zn CA D:His88 4.73 Zn OD2 D:Asp90 4.85 Zn OD1 D:Asp90 4.11 Zn CG D:Asp90 4.91 Zn NE2 D:His149 1.95 Zn ND1 D:His149 4.08 Zn CD2 D:His149 2.94 Zn CE1 D:His149 2.97 Zn CG D:His149 4.08 Zn CG2 D:Thr150 4.22 Zn CB D:Asp168 4.39 Zn OD1 D:Asp168 3.80 Zn CG D:Asp168 4.34 Zn O D:Hoh230 4.98 Zn O D:Hoh248 4.23 Zn O D:Hoh265 2.51 Zn O D:Hoh463 4.84 Zn O D:Hoh652 1.92 Zn O D:Hoh778 4.20 interactive model: