Nickel in the structure of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel (pdb 1a5n)

The binding sites of Nickel atom in the structure of K217A Variant of Klebsiella Aerogenes Urease, Chemically Rescued By Formate and Nickel (pdb code 1a5n). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1a5n structure was solved by M.A.PEARSON, R.A.SCHALLER, L.O.MICHEL, P.A.KARPLUS, R.P.HAUSINGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.4 Space group I213 a (A) 170.800 b (A) 170.800 c (A) 170.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.7 Rfree (%) n/a Nickel Binding Sites: Nickel binding site 1 out of 2 in 1a5n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1a5n. 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: His134, C: His136, C: His219, C: His246, C: Phe271, C: His272, C: Gly277, C: Asp360, C: Ni575, C: Fmt999, C: Hoh1141, C: Hoh1147, conact list: Atom Atom Distance (A) Ni NE2 C:His134 3.70 Ni ND1 C:His134 4.89 Ni CE1 C:His134 3.60 Ni NE2 C:His136 4.94 Ni NE2 C:His219 3.36 Ni CD2 C:His219 3.68 Ni CE1 C:His219 4.49 Ni CG C:His219 4.92 Ni NE2 C:His246 4.53 Ni CB C:His246 3.81 Ni ND1 C:His246 2.53 Ni CD2 C:His246 4.62 Ni CE1 C:His246 3.40 Ni CG C:His246 3.52 Ni CB C:Phe271 4.62 Ni CD2 C:Phe271 4.36 Ni CG C:Phe271 4.88 Ni NE2 C:His272 2.51 Ni ND1 C:His272 4.62 Ni CD2 C:His272 3.36 Ni CE1 C:His272 3.56 Ni CG C:His272 4.56 Ni O C:Gly277 4.10 Ni OD2 C:Asp360 4.46 Ni OD1 C:Asp360 4.75 Ni CG C:Asp360 4.96 Ni NI C:Ni575 3.01 Ni O1 C:Fmt999 1.54 Ni O2 C:Fmt999 2.79 Ni C C:Fmt999 2.51 Ni O C:Hoh1141 4.34 Ni O C:Hoh1147 3.36 interactive model: Nickel binding site 2 out of 2 in 1a5n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1a5n. 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: His134, C: His136, C: Ala167, C: Thr169, C: His219, C: His272, C: Asp360, C: Ala363, C: Ni574, C: Fmt999, C: Hoh1141, C: Hoh1147, conact list: Atom Atom Distance (A) Ni NE2 C:His134 2.31 Ni ND1 C:His134 4.30 Ni CD2 C:His134 3.29 Ni CE1 C:His134 3.18 Ni CG C:His134 4.38 Ni NE2 C:His136 2.27 Ni ND1 C:His136 4.34 Ni CD2 C:His136 3.28 Ni CE1 C:His136 3.20 Ni CG C:His136 4.41 Ni O C:Ala167 4.72 Ni CG2 C:Thr169 4.40 Ni NE2 C:His219 4.74 Ni NE2 C:His272 4.73 Ni CD2 C:His272 4.75 Ni CB C:Asp360 4.16 Ni OD2 C:Asp360 3.03 Ni OD1 C:Asp360 2.03 Ni CG C:Asp360 2.81 Ni CA C:Asp360 4.56 Ni O C:Ala363 4.11 Ni CB C:Ala363 4.43 Ni NI C:Ni574 3.01 Ni O1 C:Fmt999 3.48 Ni O2 C:Fmt999 2.22 Ni C C:Fmt999 3.18 Ni O C:Hoh1141 4.00 Ni O C:Hoh1147 1.86 interactive model: