Nickel in the structure of Crystal Structure of Substrate-Binding Periplasmic Protein (Pbp) From Ralstonia Solanacearum (pdb 3lop)

The binding sites of Nickel atom in the structure of Crystal Structure of Substrate-Binding Periplasmic Protein (Pbp) From Ralstonia Solanacearum (pdb code 3lop). This binding sites where shown with 5.0 Angstroms radius around Nickel atom. The 3lop structure was solved by K.PALANI, S.K.BURLEY, S.SWAMINATHAN, NEW YORK SGX RESEARCHCENTER FOR STRUCTURAL GENOMICS (NYSGXRC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.7-1.6 Space group P212121 a (A) 44.110 b (A) 64.739 c (A) 114.085 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) 19.5 Nickel Binding Sites: Nickel binding site 1 out of 2 in 3lop Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 3lop. 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: His344, A: Glu348, A: Hoh439, A: Hoh618, A: Hoh644, A: Hoh686, A: Hoh748, A: Hoh769, A: Hoh801, conact list: Atom Atom Distance (A) Ni NE2 A:His344 3.13 Ni ND1 A:His344 3.26 Ni CD2 A:His344 4.34 Ni CE1 A:His344 2.24 Ni CG A:His344 4.41 Ni OE1 A:Glu348 2.30 Ni CB A:Glu348 4.98 Ni OE2 A:Glu348 2.20 Ni CD A:Glu348 2.53 Ni CG A:Glu348 4.00 Ni O A:Hoh439 4.42 Ni O A:Hoh618 4.68 Ni O A:Hoh644 2.31 Ni O A:Hoh686 2.30 Ni O A:Hoh748 4.86 Ni O A:Hoh769 4.16 Ni O A:Hoh801 2.25 interactive model: Nickel binding site 2 out of 2 in 3lop Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 3lop. 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: Gly357, A: Thr359, A: His371, A: Hoh451, A: Hoh483, A: Hoh528, A: Hoh560, A: Hoh654, A: Hoh710, A: Hoh802, conact list: Atom Atom Distance (A) Ni O A:Gly357 3.78 Ni C A:Gly357 4.97 Ni OG1 A:Thr359 4.23 Ni NE2 A:His371 3.03 Ni ND1 A:His371 3.44 Ni CD2 A:His371 4.30 Ni CE1 A:His371 2.32 Ni CG A:His371 4.50 Ni O A:Hoh451 4.49 Ni O A:Hoh483 2.29 Ni O A:Hoh528 2.20 Ni O A:Hoh560 2.22 Ni O A:Hoh654 2.41 Ni O A:Hoh710 2.38 Ni O A:Hoh802 4.35 interactive model: