Sodium in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb 2pca)

The binding sites of Sodium atom in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2pca). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2pca structure was solved by M.SUGAHARA, M.TAKETA, Y.MORIKAWA, Y.MATSUURA, N.KUNISHIMA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.1-2.0 Space group P41212 a (A) 105.079 b (A) 105.079 c (A) 140.133 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.3 Rfree (%) 22.9 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2pca Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2pca. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Tyr117, A: Ile127, A: Phe130, A: Gly131, B: Tyr117, B: Phe130, B: Gly131, B: Ser133, A: Hoh608, A: Hoh609, A: Hoh633, A: Hoh775, B: Hoh274, B: Hoh276, B: Hoh280, B: Hoh311, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.62 Na CD2 A:Tyr117 4.91 Na CZ A:Tyr117 3.17 Na CE1 A:Tyr117 4.23 Na OH A:Tyr117 2.21 Na O A:Ile127 4.51 Na O A:Phe130 4.17 Na CB A:Phe130 4.31 Na C A:Phe130 4.74 Na O A:Gly131 4.80 Na CD1 B:Tyr117 4.24 Na CE1 B:Tyr117 4.33 Na O B:Phe130 4.69 Na CB B:Phe130 4.37 Na C B:Phe130 4.92 Na O B:Gly131 3.80 Na C B:Gly131 4.91 Na OG B:Ser133 4.11 Na O A:Hoh608 2.21 Na O A:Hoh609 4.21 Na O A:Hoh633 4.52 Na O A:Hoh775 2.15 Na O B:Hoh274 4.80 Na O B:Hoh276 2.74 Na O B:Hoh280 2.48 Na O B:Hoh311 4.45 interactive model: