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 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: