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 |
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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:
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