Nickel in the structure of Peptide Deformylase As NI2+ Containing Form (pdb 1bs7)
The binding sites of Nickel atom in the structure of Peptide Deformylase As NI2+ Containing Form (pdb code 1bs7). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1bs7 structure was solved by A.BECKER, I.SCHLICHTING, W.KABSCH, D.GROCHE, S.SCHULTZ, A.F.V.WAGNER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 6.0-2.5 | Space group | C121 | a (A) | 143.400 | b (A) | 64.000 | c (A) | 84.500 | alpha (°) | 90.00 | beta (°) | 123.00 | gamma (°) | 90.00 | Rfactor (%) | 20.3 | Rfree (%) | 27.2 |
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Nickel Binding Sites:Nickel binding site 1 out of 3 in 1bs7
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1bs7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gln50, A: Gly89, A: Cys90, A: Leu91, A: His132, A: Glu133, A: His136, A: Hoh2009, A: Hoh2023, A: Hoh2026, A: Hoh2034, | conact list:
Atom | Atom | Distance (A) | Ni | NE2 A:Gln50 | 3.86 | Ni | OE1 A:Gln50 | 4.15 | Ni | CD A:Gln50 | 4.20 | Ni | O A:Gly89 | 4.18 | Ni | C A:Gly89 | 4.82 | Ni | N A:Cys90 | 4.62 | Ni | CB A:Cys90 | 3.05 | Ni | SG A:Cys90 | 2.08 | Ni | C A:Cys90 | 4.36 | Ni | CA A:Cys90 | 3.46 | Ni | N A:Leu91 | 4.37 | Ni | NE2 A:His132 | 2.07 | Ni | ND1 A:His132 | 4.14 | Ni | CD2 A:His132 | 3.10 | Ni | CE1 A:His132 | 3.01 | Ni | CG A:His132 | 4.22 | Ni | OE1 A:Glu133 | 4.80 | Ni | OE2 A:Glu133 | 4.55 | Ni | NE2 A:His136 | 2.36 | Ni | ND1 A:His136 | 4.34 | Ni | CD2 A:His136 | 3.50 | Ni | CE1 A:His136 | 3.13 | Ni | CG A:His136 | 4.55 | Ni | O A:Hoh2009 | 4.30 | Ni | O A:Hoh2023 | 3.24 | Ni | O A:Hoh2026 | 3.87 | Ni | O A:Hoh2034 | 2.52 |
| interactive model:
| Nickel binding site 2 out of 3 in 1bs7
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1bs7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Gln550, B: Gly589, B: Cys590, B: Leu591, B: His632, B: Glu633, B: His636, B: Hoh4, B: Hoh60, B: Hoh97, B: Hoh114, B: Hoh3004, | conact list:
Atom | Atom | Distance (A) | Ni | NE2 B:Gln550 | 3.70 | Ni | OE1 B:Gln550 | 3.92 | Ni | CD B:Gln550 | 3.97 | Ni | O B:Gly589 | 4.53 | Ni | CB B:Cys590 | 3.38 | Ni | SG B:Cys590 | 2.20 | Ni | C B:Cys590 | 4.69 | Ni | CA B:Cys590 | 3.84 | Ni | N B:Leu591 | 4.61 | Ni | NE2 B:His632 | 2.18 | Ni | ND1 B:His632 | 4.27 | Ni | CD2 B:His632 | 3.05 | Ni | CE1 B:His632 | 3.21 | Ni | CG B:His632 | 4.23 | Ni | OE1 B:Glu633 | 4.53 | Ni | OE2 B:Glu633 | 4.39 | Ni | CD B:Glu633 | 4.86 | Ni | NE2 B:His636 | 1.99 | Ni | ND1 B:His636 | 3.98 | Ni | CD2 B:His636 | 3.14 | Ni | CE1 B:His636 | 2.79 | Ni | CG B:His636 | 4.17 | Ni | O B:Hoh4 | 4.50 | Ni | O B:Hoh60 | 3.73 | Ni | O B:Hoh97 | 4.91 | Ni | O B:Hoh114 | 3.46 | Ni | O B:Hoh3004 | 1.93 |
| interactive model:
| Nickel binding site 3 out of 3 in 1bs7
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 1bs7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Gln1050, C: Gly1089, C: Cys1090, C: Leu1091, C: His1132, C: Glu1133, C: His1136, C: Hoh43, C: Hoh51, C: Hoh102, C: Hoh3005, | conact list:
Atom | Atom | Distance (A) | Ni | NE2 C:Gln1050 | 3.69 | Ni | OE1 C:Gln1050 | 3.92 | Ni | CD C:Gln1050 | 3.95 | Ni | O C:Gly1089 | 4.45 | Ni | N C:Cys1090 | 4.89 | Ni | CB C:Cys1090 | 3.30 | Ni | SG C:Cys1090 | 2.15 | Ni | C C:Cys1090 | 4.54 | Ni | CA C:Cys1090 | 3.70 | Ni | N C:Leu1091 | 4.44 | Ni | NE2 C:His1132 | 2.20 | Ni | ND1 C:His1132 | 4.30 | Ni | CD2 C:His1132 | 3.12 | Ni | CE1 C:His1132 | 3.22 | Ni | CG C:His1132 | 4.29 | Ni | OE1 C:Glu1133 | 4.62 | Ni | OE2 C:Glu1133 | 4.42 | Ni | CD C:Glu1133 | 4.90 | Ni | NE2 C:His1136 | 2.13 | Ni | ND1 C:His1136 | 4.12 | Ni | CD2 C:His1136 | 3.27 | Ni | CE1 C:His1136 | 2.93 | Ni | CG C:His1136 | 4.31 | Ni | O C:Hoh43 | 3.72 | Ni | O C:Hoh51 | 4.81 | Ni | O C:Hoh102 | 4.65 | Ni | O C:Hoh3005 | 2.16 |
| interactive model:
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