Nickel in the structure of Crystal Structure of Helicobacter Pylori Urease in Complex With Acetohydroxamic Acid (pdb 1e9y)

The binding sites of Nickel atom in the structure of Crystal Structure of Helicobacter Pylori Urease in Complex With Acetohydroxamic Acid (pdb code 1e9y). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 1e9y structure was solved by N.-C.HA, S.-T.OH, B.-H.OH, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-3.0 Space group I23 a (A) 178.160 b (A) 178.160 c (A) 178.160 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.3 Rfree (%) 28.2 Nickel Binding Sites: Nickel binding site 1 out of 2 in 1e9y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1e9y. 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: His136, B: His138, B: Ala169, B: Kcx219, B: His221, B: His248, B: His274, B: Gly279, B: Asp362, B: Hae800, B: Ni3002, conact list: Atom Atom Distance (A) Ni NE2 B:His136 3.89 Ni CE1 B:His136 4.09 Ni NE2 B:His138 4.96 Ni O B:Ala169 4.99 Ni OQ1 B:Kcx219 2.41 Ni CX B:Kcx219 2.89 Ni OQ2 B:Kcx219 2.56 Ni NZ B:Kcx219 4.21 Ni NE2 B:His221 3.95 Ni CD2 B:His221 4.04 Ni NE2 B:His248 4.14 Ni CB B:His248 4.21 Ni ND1 B:His248 2.39 Ni CD2 B:His248 4.48 Ni CE1 B:His248 2.91 Ni CG B:His248 3.60 Ni NE2 B:His274 2.38 Ni ND1 B:His274 4.52 Ni CD2 B:His274 3.09 Ni CE1 B:His274 3.52 Ni CG B:His274 4.35 Ni O B:Gly279 3.49 Ni C B:Gly279 4.46 Ni OD2 B:Asp362 4.69 Ni OD1 B:Asp362 4.70 Ni CG B:Asp362 4.98 Ni O B:Hae800 2.39 Ni O2 B:Hae800 2.48 Ni N B:Hae800 3.21 Ni C2 B:Hae800 3.20 Ni C1 B:Hae800 4.69 Ni NI B:Ni3002 3.02 interactive model: Nickel binding site 2 out of 2 in 1e9y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1e9y. 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: His136, B: His138, B: Ala169, B: Thr171, B: Kcx219, B: His274, B: Asp362, B: Ala365, B: Hae800, B: Ni3001, conact list: Atom Atom Distance (A) Ni NE2 B:His136 2.35 Ni ND1 B:His136 4.37 Ni CD2 B:His136 3.24 Ni CE1 B:His136 3.30 Ni CG B:His136 4.37 Ni NE2 B:His138 2.16 Ni ND1 B:His138 4.17 Ni CD2 B:His138 3.24 Ni CE1 B:His138 3.00 Ni CG B:His138 4.31 Ni O B:Ala169 4.71 Ni CG2 B:Thr171 3.75 Ni OQ1 B:Kcx219 3.23 Ni CX B:Kcx219 2.92 Ni OQ2 B:Kcx219 2.40 Ni NZ B:Kcx219 3.78 Ni NE2 B:His274 4.83 Ni CD2 B:His274 4.81 Ni CB B:Asp362 4.35 Ni OD2 B:Asp362 2.36 Ni OD1 B:Asp362 3.74 Ni CG B:Asp362 3.26 Ni CA B:Asp362 4.66 Ni O B:Ala365 4.75 Ni O B:Hae800 2.57 Ni O2 B:Hae800 3.88 Ni N B:Hae800 3.33 Ni C2 B:Hae800 3.90 Ni NI B:Ni3001 3.02 interactive model: