Sodium in the structure of Crystal Structure of the PH0510 Protein From Pyrococcus Horikoshii OT3 (pdb 2dec)

The binding sites of Sodium atom in the structure of Crystal Structure of the PH0510 Protein From Pyrococcus Horikoshii OT3 (pdb code 2dec). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2dec structure was solved by H.MIZUTANI, N.KUNISHIMA, RIKEN STRUCTURAL GENOMICS/PROTEOMICSINITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.7 Space group P1211 a (A) 61.228 b (A) 79.485 c (A) 67.497 alpha (°) 90.00 beta (°) 105.15 gamma (°) 90.00 Rfactor (%) 16.6 Rfree (%) 18.9 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2dec Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2dec. 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: Ser42, A: Ile86, A: Ser87, A: Arg88, A: Ser89, A: Thr92, A: Hoh905, A: Hoh911, A: Hoh920, A: Hoh948, A: Hoh949, A: Hoh1004, A: Hoh1124, B: Hoh852, conact list: Atom Atom Distance (A) Na OG A:Ser42 4.50 Na O A:Ile86 4.91 Na O A:Ser87 4.94 Na N A:Ser87 4.89 Na CB A:Ser87 3.72 Na OG A:Ser87 3.03 Na C A:Ser87 3.87 Na CA A:Ser87 3.57 Na N A:Arg88 3.44 Na CB A:Arg88 4.54 Na C A:Arg88 4.93 Na CA A:Arg88 4.46 Na N A:Ser89 4.28 Na OG A:Ser89 4.26 Na CB A:Thr92 4.08 Na CG2 A:Thr92 4.70 Na OG1 A:Thr92 2.78 Na O A:Hoh905 3.72 Na O A:Hoh911 2.10 Na O A:Hoh920 3.31 Na O A:Hoh948 4.43 Na O A:Hoh949 2.11 Na O A:Hoh1004 2.21 Na O A:Hoh1124 3.99 Na O B:Hoh852 3.92 interactive model: