Sodium in the structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. (pdb 2gyq)

The binding sites of Sodium atom in the structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. (pdb code 2gyq). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2gyq structure was solved by J.OSIPIUK, E.EVDOKIMOVA, M.KUDRITSKA, A.SAVCHENKO, A.EDWARDS, A.JOACHIMIAK, MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.7-1.4 Space group P212121 a (A) 33.451 b (A) 101.125 c (A) 103.802 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14 Rfree (%) 17.6 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2gyq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2gyq. 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: Phe3, A: Phe4, A: Ser5, A: Asp7, A: Hoh547, A: Hoh548, conact list: Atom Atom Distance (A) Na O A:Phe3 4.57 Na C A:Phe4 4.86 Na CA A:Phe4 4.74 Na CA A:Phe4 4.84 Na O A:Ser5 4.21 Na N A:Ser5 4.91 Na CB A:Asp7 4.08 Na OD2 A:Asp7 2.07 Na OD1 A:Asp7 2.44 Na CG A:Asp7 2.58 Na CA A:Asp7 4.95 Na O A:Hoh547 2.18 Na O A:Hoh548 4.38 interactive model: