Nickel in the structure of Peptide Deformylase As NI2+ Containing Form in Complex With Tripeptide Met-Ala-Ser (pdb 1bs6)

The binding sites of Nickel atom in the structure of Peptide Deformylase As NI2+ Containing Form in Complex With Tripeptide Met-Ala-Ser (pdb code 1bs6). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1bs6 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) 6.0-2.1 Space group C121 a (A) 143.800 b (A) 64.100 c (A) 85.100 alpha (°) 90.00 beta (°) 123.30 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 25.8 Nickel Binding Sites: Nickel binding site 1 out of 3 in 1bs6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1bs6. 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: Ser92, A: His132, A: Glu133, A: His136, D: Met1, A: Hoh2005, A: Hoh2037, A: Hoh2041, A: Hoh2042, conact list: Atom Atom Distance (A) Ni NE2 A:Gln50 3.71 Ni OE1 A:Gln50 4.08 Ni CD A:Gln50 4.06 Ni O A:Gly89 4.63 Ni N A:Cys90 4.90 Ni CB A:Cys90 3.35 Ni SG A:Cys90 2.41 Ni C A:Cys90 4.44 Ni CA A:Cys90 3.68 Ni N A:Leu91 4.28 Ni OG A:Ser92 4.96 Ni NE2 A:His132 2.19 Ni ND1 A:His132 4.23 Ni CD2 A:His132 3.21 Ni CE1 A:His132 3.10 Ni CG A:His132 4.32 Ni OE1 A:Glu133 4.72 Ni NE2 A:His136 2.34 Ni ND1 A:His136 4.34 Ni CD2 A:His136 3.46 Ni CE1 A:His136 3.14 Ni CG A:His136 4.52 Ni N D:Met1 4.13 Ni CA D:Met1 4.36 Ni O A:Hoh2005 4.75 Ni O A:Hoh2037 3.69 Ni O A:Hoh2041 2.17 Ni O A:Hoh2042 2.30 interactive model: Nickel binding site 2 out of 3 in 1bs6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1bs6. 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, E: Met1, B: Hoh5, B: Hoh22, E: Hoh137, E: Hoh3005, conact list: Atom Atom Distance (A) Ni NE2 B:Gln550 3.46 Ni OE1 B:Gln550 3.91 Ni CD B:Gln550 3.94 Ni O B:Gly589 4.63 Ni CB B:Cys590 3.34 Ni SG B:Cys590 2.26 Ni C B:Cys590 4.66 Ni CA B:Cys590 3.86 Ni N B:Leu591 4.55 Ni NE2 B:His632 2.17 Ni ND1 B:His632 4.19 Ni CD2 B:His632 3.13 Ni CE1 B:His632 3.10 Ni CG B:His632 4.25 Ni OE1 B:Glu633 4.56 Ni OE2 B:Glu633 4.19 Ni CD B:Glu633 4.76 Ni NE2 B:His636 2.23 Ni ND1 B:His636 4.20 Ni CD2 B:His636 3.36 Ni CE1 B:His636 3.01 Ni CG B:His636 4.40 Ni N E:Met1 3.42 Ni CB E:Met1 5.00 Ni CA E:Met1 4.04 Ni O B:Hoh5 4.85 Ni O B:Hoh22 3.83 Ni O E:Hoh137 3.37 Ni O E:Hoh3005 1.92 interactive model: Nickel binding site 3 out of 3 in 1bs6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Nickel in the PDB 1bs6. 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, F: Met1, C: Hoh31, C: Hoh56, C: Hoh3006, C: Hoh3007, conact list: Atom Atom Distance (A) Ni NE2 C:Gln1050 3.67 Ni OE1 C:Gln1050 3.92 Ni CD C:Gln1050 3.99 Ni O C:Gly1089 4.65 Ni N C:Cys1090 4.99 Ni CB C:Cys1090 3.48 Ni SG C:Cys1090 2.44 Ni C C:Cys1090 4.55 Ni CA C:Cys1090 3.76 Ni N C:Leu1091 4.47 Ni NE2 C:His1132 2.17 Ni ND1 C:His1132 4.23 Ni CD2 C:His1132 3.17 Ni CE1 C:His1132 3.10 Ni CG C:His1132 4.30 Ni OE1 C:Glu1133 4.52 Ni OE2 C:Glu1133 4.51 Ni CD C:Glu1133 4.89 Ni NE2 C:His1136 2.22 Ni ND1 C:His1136 4.29 Ni CD2 C:His1136 3.24 Ni CE1 C:His1136 3.15 Ni CG C:His1136 4.37 Ni N F:Met1 4.18 Ni CA F:Met1 4.12 Ni O C:Hoh31 3.82 Ni O C:Hoh56 4.71 Ni O C:Hoh3006 2.05 Ni O C:Hoh3007 2.69 interactive model: