Nickel in the structure of Crystal Structure of Human JMJD2C Catalytic Domain (pdb 2xml)

The binding sites of Nickel atom in the structure of Crystal Structure of Human JMJD2C Catalytic Domain (pdb code 2xml). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 2xml structure was solved by W.W.YUE, C.GILEADI, T.KROJER, A.C.W.PIKE, F.VONDELFT, S.NG, L.CARPENTER, C.ARROWSMITH, J.WEIGELT, A.EDWARDS, C.BOUNTRA, U.OPPERMANN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.6-2.5 Space group P22121 a (A) 88.660 b (A) 95.870 c (A) 100.690 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.61 Rfree (%) 25.4 Nickel Binding Sites: Nickel binding site 1 out of 2 in 2xml Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 2xml. 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: His190, A: Glu192, A: Ser198, A: Thr272, A: His278, A: Oga601, A: Hoh2084, conact list: Atom Atom Distance (A) Ni NE2 A:His190 2.22 Ni ND1 A:His190 4.17 Ni CD2 A:His190 3.28 Ni CE1 A:His190 3.02 Ni CG A:His190 4.33 Ni OE1 A:Glu192 3.36 Ni OE2 A:Glu192 2.18 Ni CD A:Glu192 3.09 Ni CG A:Glu192 4.44 Ni CB A:Ser198 4.84 Ni OG A:Ser198 4.13 Ni CG2 A:Thr272 4.90 Ni OG1 A:Thr272 4.93 Ni NE2 A:His278 2.17 Ni ND1 A:His278 4.13 Ni CD2 A:His278 3.33 Ni CE1 A:His278 2.93 Ni CG A:His278 4.36 Ni N1 A:Oga601 4.24 Ni O2 A:Oga601 4.24 Ni C4 A:Oga601 4.97 Ni C1 A:Oga601 2.97 Ni O1 A:Oga601 2.33 Ni O2' A:Oga601 2.24 Ni C2 A:Oga601 2.98 Ni O A:Hoh2084 2.06 interactive model: Nickel binding site 2 out of 2 in 2xml Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 2xml. 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: B: His190, B: Glu192, B: Ser198, B: Lys243, B: Thr272, B: His278, B: Oga601, B: Hoh2072, conact list: Atom Atom Distance (A) Ni NE2 B:His190 2.12 Ni ND1 B:His190 4.08 Ni CD2 B:His190 3.18 Ni CE1 B:His190 2.95 Ni CG B:His190 4.23 Ni OE1 B:Glu192 3.34 Ni OE2 B:Glu192 2.15 Ni CD B:Glu192 3.07 Ni CG B:Glu192 4.43 Ni CB B:Ser198 4.93 Ni OG B:Ser198 4.21 Ni NZ B:Lys243 4.95 Ni CG2 B:Thr272 4.96 Ni OG1 B:Thr272 4.99 Ni NE2 B:His278 2.16 Ni ND1 B:His278 4.11 Ni CD2 B:His278 3.33 Ni CE1 B:His278 2.89 Ni CG B:His278 4.35 Ni N1 B:Oga601 4.18 Ni O2 B:Oga601 4.16 Ni C4 B:Oga601 4.88 Ni C1 B:Oga601 2.93 Ni O1 B:Oga601 2.20 Ni O2' B:Oga601 2.20 Ni C2 B:Oga601 2.88 Ni O B:Hoh2072 2.24 interactive model: