Nickel in the structure of Crystal Structure Of the D221A Variant of Klebsiella Aerogenes Urease (pdb 1ejr)

The binding sites of Nickel atom in the structure of Crystal Structure Of the D221A Variant of Klebsiella Aerogenes Urease (pdb code 1ejr). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1ejr structure was solved by M.A.PEARSON, I.S.PARK, 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) 10.0-2.0 Space group I213 a (A) 170.600 b (A) 170.600 c (A) 170.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) n/a Nickel Binding Sites: Nickel binding site 1 out of 2 in 1ejr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1ejr. 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: His1134, C: Kcx1217, C: His1219, C: His1246, C: His1272, C: Gly1277, C: Asp1360, C: Ni4775, C: Hoh170, C: Hoh500, C: Hoh501, C: Hoh502, conact list: Atom Atom Distance (A) Ni NE2 C:His1134 4.28 Ni CE1 C:His1134 4.18 Ni OQ1 C:Kcx1217 2.04 Ni CX C:Kcx1217 3.04 Ni CE C:Kcx1217 4.76 Ni OQ2 C:Kcx1217 3.33 Ni NZ C:Kcx1217 4.23 Ni NE2 C:His1219 3.59 Ni CD2 C:His1219 3.83 Ni CE1 C:His1219 4.69 Ni NE2 C:His1246 4.07 Ni CB C:His1246 3.64 Ni ND1 C:His1246 2.09 Ni CD2 C:His1246 4.22 Ni CE1 C:His1246 2.91 Ni CG C:His1246 3.18 Ni CA C:His1246 4.83 Ni NE2 C:His1272 2.25 Ni ND1 C:His1272 4.34 Ni CD2 C:His1272 3.20 Ni CE1 C:His1272 3.23 Ni CG C:His1272 4.36 Ni O C:Gly1277 3.42 Ni C C:Gly1277 4.52 Ni OD2 C:Asp1360 4.55 Ni NI C:Ni4775 3.57 Ni O C:Hoh170 4.15 Ni O C:Hoh500 2.06 Ni O C:Hoh501 2.54 Ni O C:Hoh502 3.62 interactive model: Nickel binding site 2 out of 2 in 1ejr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1ejr. 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: His1134, C: His1136, C: Ala1167, C: Thr1169, C: Kcx1217, C: His1272, C: Asp1360, C: Ala1363, C: Ni4774, C: Hoh170, C: Hoh500, C: Hoh501, C: Hoh502, conact list: Atom Atom Distance (A) Ni NE2 C:His1134 2.21 Ni ND1 C:His1134 4.24 Ni CD2 C:His1134 3.15 Ni CE1 C:His1134 3.16 Ni CG C:His1134 4.28 Ni NE2 C:His1136 2.11 Ni ND1 C:His1136 4.17 Ni CD2 C:His1136 3.16 Ni CE1 C:His1136 3.03 Ni CG C:His1136 4.27 Ni O C:Ala1167 4.45 Ni CG2 C:Thr1169 4.15 Ni OQ1 C:Kcx1217 3.51 Ni CX C:Kcx1217 3.17 Ni OQ2 C:Kcx1217 2.19 Ni NZ C:Kcx1217 4.29 Ni NE2 C:His1272 4.92 Ni CD2 C:His1272 4.95 Ni CB C:Asp1360 4.26 Ni OD2 C:Asp1360 3.34 Ni OD1 C:Asp1360 2.12 Ni CG C:Asp1360 2.99 Ni CA C:Asp1360 4.54 Ni O C:Ala1363 4.30 Ni CB C:Ala1363 4.40 Ni NI C:Ni4774 3.57 Ni O C:Hoh170 4.62 Ni O C:Hoh500 2.10 Ni O C:Hoh501 3.56 Ni O C:Hoh502 2.41 interactive model: