Sodium in the structure of Crystal Structure Of LEU65 to Arg Mutant of Diphthine Synthase (pdb 2dv3)

The binding sites of Sodium atom in the structure of Crystal Structure Of LEU65 to Arg Mutant of Diphthine Synthase (pdb code 2dv3). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2dv3 structure was solved by H.MIZUTANI, Y.MATSUURA, N.KUNISHIMA, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.9 Space group P41212 a (A) 104.197 b (A) 104.197 c (A) 137.827 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.9 Rfree (%) 23.4 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2dv3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2dv3. 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: Hoh1305, A: Hoh1307, A: Hoh1374, B: Hoh1503, B: Hoh1504, B: Hoh1505, B: Hoh1507, B: Hoh1516, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.73 Na CZ A:Tyr117 3.34 Na CE1 A:Tyr117 4.42 Na OH A:Tyr117 2.39 Na O A:Ile127 4.30 Na O A:Phe130 4.13 Na CB A:Phe130 4.36 Na C A:Phe130 4.75 Na O A:Gly131 4.89 Na CD1 B:Tyr117 4.17 Na CE1 B:Tyr117 4.27 Na O B:Phe130 4.78 Na CB B:Phe130 4.41 Na O B:Gly131 3.92 Na OG B:Ser133 4.03 Na O A:Hoh1305 4.31 Na O A:Hoh1307 4.51 Na O A:Hoh1374 2.07 Na O B:Hoh1503 2.57 Na O B:Hoh1504 4.39 Na O B:Hoh1505 4.71 Na O B:Hoh1507 2.17 Na O B:Hoh1516 2.54 interactive model: