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

The binding sites of Sodium atom in the structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2huv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2huv structure was solved by M.SUGAHARA, K.SARABOJI, S.M.MALATHY SONY, M.N.PONNUSWAMY, T.S.KUMAREVEL, N.KUNISHIMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 12.0-2.1 Space group P41212 a (A) 104.731 b (A) 104.731 c (A) 137.513 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 22.7 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2huv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2huv. 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: Hoh3002, A: Hoh3007, A: Hoh3034, A: Hoh3125, B: Hoh2004, B: Hoh2007, B: Hoh2008, B: Hoh2043, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.69 Na CD2 A:Tyr117 4.99 Na CZ A:Tyr117 3.36 Na CE1 A:Tyr117 4.47 Na OH A:Tyr117 2.45 Na O A:Ile127 4.13 Na O A:Phe130 4.18 Na CB A:Phe130 4.44 Na C A:Phe130 4.85 Na O A:Gly131 4.99 Na CD1 B:Tyr117 4.22 Na CE1 B:Tyr117 4.39 Na O B:Phe130 4.82 Na CB B:Phe130 4.46 Na O B:Gly131 3.77 Na C B:Gly131 4.90 Na OG B:Ser133 3.88 Na O A:Hoh3002 2.13 Na O A:Hoh3007 4.57 Na O A:Hoh3034 4.52 Na O A:Hoh3125 2.06 Na O B:Hoh2004 4.60 Na O B:Hoh2007 2.29 Na O B:Hoh2008 2.56 Na O B:Hoh2043 4.29 interactive model: