Sodium in the structure of Mutant L65M Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb 2emr)

The binding sites of Sodium atom in the structure of Mutant L65M Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2emr). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2emr structure was solved by K.SHIMIZU, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.4 Space group P41212 a (A) 105.597 b (A) 105.597 c (A) 139.682 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 22.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2emr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2emr. 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: Hoh312, A: Hoh313, A: Hoh405, A: Hoh445, B: Hoh269, B: Hoh274, B: Hoh276, B: Hoh305, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.85 Na CZ A:Tyr117 3.23 Na CE1 A:Tyr117 4.15 Na OH A:Tyr117 2.23 Na O A:Ile127 4.28 Na O A:Phe130 4.02 Na CB A:Phe130 4.19 Na C A:Phe130 4.68 Na CA A:Phe130 4.99 Na O A:Gly131 4.80 Na CD1 B:Tyr117 4.22 Na CE1 B:Tyr117 4.30 Na O B:Phe130 4.88 Na CB B:Phe130 4.52 Na O B:Gly131 3.86 Na C B:Gly131 4.97 Na OG B:Ser133 4.19 Na O A:Hoh312 2.15 Na O A:Hoh313 4.38 Na O A:Hoh405 4.40 Na O A:Hoh445 2.34 Na O B:Hoh269 2.49 Na O B:Hoh274 4.82 Na O B:Hoh276 2.54 Na O B:Hoh305 4.28 interactive model: