Nickel in the structure of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure (pdb 1s3t)

The binding sites of Nickel atom in the structure of Borate Inhibited Bacillus Pasteurii Urease Crystal Structure (pdb code 1s3t). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1s3t structure was solved by S.BENINI, W.R.RYPNIEWSKI, K.S.WILSON, S.CIURLI, S.MANGANI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.8-2.1 Space group P6322 a (A) 130.906 b (A) 130.906 c (A) 189.366 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 17.7 Rfree (%) 20.5 Nickel Binding Sites: Nickel binding site 1 out of 2 in 1s3t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1s3t. 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: His137, C: Kcx220, C: His222, C: His249, C: His275, C: Gly280, C: Asp363, C: Ni601, C: So4603, C: Bo3602, C: Hoh604, conact list: Atom Atom Distance (A) Ni NE2 C:His137 4.15 Ni CE1 C:His137 3.93 Ni OQ1 C:Kcx220 2.03 Ni CX C:Kcx220 3.08 Ni CE C:Kcx220 4.74 Ni OQ2 C:Kcx220 3.42 Ni NZ C:Kcx220 4.26 Ni NE2 C:His222 3.57 Ni CD2 C:His222 3.88 Ni CE1 C:His222 4.63 Ni NE2 C:His249 4.19 Ni CB C:His249 3.51 Ni ND1 C:His249 2.12 Ni CD2 C:His249 4.27 Ni CE1 C:His249 3.05 Ni CG C:His249 3.16 Ni CA C:His249 4.76 Ni NE2 C:His275 2.07 Ni ND1 C:His275 4.15 Ni CD2 C:His275 3.06 Ni CE1 C:His275 3.03 Ni CG C:His275 4.19 Ni O C:Gly280 3.39 Ni C C:Gly280 4.34 Ni OD2 C:Asp363 4.30 Ni OD1 C:Asp363 4.96 Ni NI C:Ni601 3.61 Ni O2 C:So4603 4.53 Ni O1 C:Bo3602 3.55 Ni O2 C:Bo3602 2.19 Ni O3 C:Bo3602 3.55 Ni B C:Bo3602 2.86 Ni O C:Hoh604 1.99 interactive model: Nickel binding site 2 out of 2 in 1s3t Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1s3t. 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: His137, C: His139, C: Ala170, C: Thr172, C: Kcx220, C: His275, C: Asp363, C: Ala366, C: Ni600, C: Bo3602, C: Hoh604, conact list: Atom Atom Distance (A) Ni NE2 C:His137 2.09 Ni ND1 C:His137 4.17 Ni CD2 C:His137 3.03 Ni CE1 C:His137 3.07 Ni CG C:His137 4.18 Ni NE2 C:His139 2.17 Ni ND1 C:His139 4.19 Ni CD2 C:His139 3.27 Ni CE1 C:His139 3.01 Ni CG C:His139 4.34 Ni O C:Ala170 4.35 Ni N C:Thr172 4.94 Ni CG2 C:Thr172 4.13 Ni OQ1 C:Kcx220 3.31 Ni CX C:Kcx220 3.01 Ni OQ2 C:Kcx220 2.08 Ni NZ C:Kcx220 4.14 Ni NE2 C:His275 4.81 Ni CD2 C:His275 4.89 Ni CB C:Asp363 4.42 Ni OD2 C:Asp363 3.34 Ni OD1 C:Asp363 2.23 Ni CG C:Asp363 3.11 Ni CA C:Asp363 4.64 Ni CB C:Ala366 4.10 Ni NI C:Ni600 3.61 Ni O1 C:Bo3602 2.12 Ni O2 C:Bo3602 3.67 Ni O3 C:Bo3602 3.72 Ni B C:Bo3602 2.95 Ni O C:Hoh604 2.17 interactive model: