The binding sites of Nickel atom in the structure of Crystal Structure Of the H320Q Variant of Klebsiella Aerogenes Urease (pdb code 1ejv). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1ejv 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) | 10.0-2.4 | 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 (%) | 18.1 | Rfree (%) | n/a |
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Nickel binding site 1 out of 2 in 1ejv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1ejv. 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: Gly1278, C: Asp1360, C: Ni4775, C: Hoh170, C: Hoh500, C: Hoh501, C: Hoh502, | conact list:
Atom | Atom | Distance (A) | Ni | NE2 C:His1134 | 4.49 | Ni | CE1 C:His1134 | 4.25 | Ni | OQ1 C:Kcx1217 | 2.08 | Ni | CX C:Kcx1217 | 3.07 | Ni | CE C:Kcx1217 | 4.76 | Ni | OQ2 C:Kcx1217 | 3.38 | Ni | NZ C:Kcx1217 | 4.24 | Ni | NE2 C:His1219 | 3.65 | Ni | CD2 C:His1219 | 4.01 | Ni | CE1 C:His1219 | 4.64 | Ni | NE2 C:His1246 | 4.02 | Ni | CB C:His1246 | 3.61 | Ni | ND1 C:His1246 | 2.01 | Ni | CD2 C:His1246 | 4.18 | Ni | CE1 C:His1246 | 2.84 | Ni | CG C:His1246 | 3.14 | Ni | CA C:His1246 | 4.77 | Ni | NE2 C:His1272 | 2.16 | Ni | ND1 C:His1272 | 4.21 | Ni | CD2 C:His1272 | 3.16 | Ni | CE1 C:His1272 | 3.09 | Ni | CG C:His1272 | 4.28 | Ni | O C:Gly1277 | 3.31 | Ni | C C:Gly1277 | 4.44 | Ni | CA C:Gly1278 | 4.94 | Ni | OD2 C:Asp1360 | 4.81 | Ni | NI C:Ni4775 | 3.71 | Ni | O C:Hoh170 | 4.24 | Ni | O C:Hoh500 | 2.21 | Ni | O C:Hoh501 | 1.95 | Ni | O C:Hoh502 | 4.02 |
| interactive model:
| Nickel binding site 2 out of 2 in 1ejv
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1ejv. 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 | 2.14 | Ni | ND1 C:His1134 | 4.14 | Ni | CD2 C:His1134 | 3.18 | Ni | CE1 C:His1134 | 3.01 | Ni | CG C:His1134 | 4.26 | Ni | NE2 C:His1136 | 2.19 | Ni | ND1 C:His1136 | 4.27 | Ni | CD2 C:His1136 | 3.18 | Ni | CE1 C:His1136 | 3.15 | Ni | CG C:His1136 | 4.32 | Ni | O C:Ala1167 | 4.62 | Ni | CG2 C:Thr1169 | 4.32 | Ni | OQ1 C:Kcx1217 | 3.58 | Ni | CX C:Kcx1217 | 3.25 | Ni | OQ2 C:Kcx1217 | 2.29 | Ni | NZ C:Kcx1217 | 4.38 | Ni | NE2 C:His1272 | 4.87 | Ni | CD2 C:His1272 | 4.86 | Ni | CB C:Asp1360 | 4.22 | Ni | OD2 C:Asp1360 | 3.36 | Ni | OD1 C:Asp1360 | 2.22 | Ni | CG C:Asp1360 | 3.01 | Ni | CA C:Asp1360 | 4.53 | Ni | O C:Ala1363 | 4.33 | Ni | CB C:Ala1363 | 4.44 | Ni | NI C:Ni4774 | 3.71 | Ni | O C:Hoh170 | 4.58 | Ni | O C:Hoh500 | 2.11 | Ni | O C:Hoh501 | 3.38 | Ni | O C:Hoh502 | 3.08 |
| interactive model:
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