Sodium in the structure of The Structure of Ycin, An Unchracterized Protein From Shigella Flexneri. (pdb 3m92)

The binding sites of Sodium atom in the structure of The Structure of Ycin, An Unchracterized Protein From Shigella Flexneri. (pdb code 3m92). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3m92 structure was solved by M.E.CUFF, X.XU, H.CUI, S.CHIN, A.SAVCHENKO, A.EDWARDS, A.JOACHIMIAK, MIDWESTCENTER FOR STRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.2-2.0 Space group P3221 a (A) 56.350 b (A) 56.350 c (A) 132.260 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.8 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3m92 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3m92. 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: Thr5, B: Gln38, B: Gly41, B: Leu75, B: Ser76, B: Glu77, B: Tyr79, B: His80, A: Hoh98, B: Hoh130, B: Hoh133, conact list: Atom Atom Distance (A) Na CB A:Thr5 4.71 Na CG2 A:Thr5 4.36 Na OG1 A:Thr5 4.41 Na OE1 B:Gln38 4.52 Na O B:Gly41 4.02 Na O B:Leu75 4.91 Na O B:Ser76 2.37 Na N B:Ser76 4.99 Na CB B:Ser76 3.98 Na OG B:Ser76 4.69 Na C B:Ser76 3.34 Na CA B:Ser76 3.63 Na N B:Glu77 4.56 Na O B:Tyr79 2.49 Na N B:Tyr79 4.69 Na C B:Tyr79 3.59 Na CA B:Tyr79 4.73 Na N B:His80 4.25 Na CB B:His80 4.23 Na CA B:His80 4.16 Na O A:Hoh98 2.42 Na O B:Hoh130 2.30 Na O B:Hoh133 2.22 interactive model: