Nickel in the structure of X-Ray Structure of Human Cyclophilin J At 2.0 Angstrom (pdb 2ok3)

The binding sites of Nickel atom in the structure of X-Ray Structure of Human Cyclophilin J At 2.0 Angstrom (pdb code 2ok3). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 2ok3 structure was solved by Z.XIA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.1-2.0 Space group P3121 a (A) 40.577 b (A) 40.577 c (A) 170.682 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.2 Rfree (%) 25.5 Nickel Binding Sites: Nickel binding site 1 out of 2 in 2ok3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 2ok3. 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: His6, A: Asp11, A: Asp151, A: Hoh936, A: Hoh948, A: Hoh953, A: Hoh955, A: Hoh961, conact list: Atom Atom Distance (A) Ni NE2 A:His6 4.44 Ni CB A:His6 3.55 Ni ND1 A:His6 2.36 Ni CD2 A:His6 4.46 Ni CE1 A:His6 3.32 Ni CG A:His6 3.31 Ni CA A:His6 4.67 Ni OD2 A:Asp11 4.02 Ni OD1 A:Asp11 3.99 Ni CG A:Asp11 4.42 Ni OD1 A:Asp151 4.70 Ni O A:Hoh936 2.22 Ni O A:Hoh948 2.10 Ni O A:Hoh953 3.39 Ni O A:Hoh955 2.65 Ni O A:Hoh961 2.81 interactive model: Nickel binding site 2 out of 2 in 2ok3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 2ok3. 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: Ile41, A: Asp146, A: His148, A: Hoh867, A: Hoh922, A: Hoh937, A: Hoh938, A: Hoh939, A: Hoh940, conact list: Atom Atom Distance (A) Ni CG2 A:Ile41 4.74 Ni CB A:Asp146 4.54 Ni OD2 A:Asp146 4.01 Ni CG A:Asp146 4.73 Ni NE2 A:His148 2.09 Ni ND1 A:His148 4.19 Ni CD2 A:His148 2.97 Ni CE1 A:His148 3.14 Ni CG A:His148 4.15 Ni O A:Hoh867 4.03 Ni O A:Hoh922 4.08 Ni O A:Hoh937 2.50 Ni O A:Hoh938 2.29 Ni O A:Hoh939 2.33 Ni O A:Hoh940 2.03 interactive model: