Sodium in the structure of Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L8M) (pdb 2ek4)

The binding sites of Sodium atom in the structure of Structural Study of Project Id PH0725 From Pyrococcus Horikoshii OT3 (L8M) (pdb code 2ek4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2ek4 structure was solved by Y.ASADA, H.SHIMADA, M.TAKETA, 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) 19.7-2.2 Space group P41212 a (A) 104.662 b (A) 104.662 c (A) 138.375 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 23 Sodium Binding Sites: Sodium binding site 1 out of 1 in 2ek4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2ek4. 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: Hoh303, A: Hoh310, A: Hoh546, B: Hoh266, B: Hoh267, B: Hoh270, B: Hoh275, B: Hoh277, conact list: Atom Atom Distance (A) Na CE2 A:Tyr117 3.68 Na CD2 A:Tyr117 4.95 Na CZ A:Tyr117 3.30 Na CE1 A:Tyr117 4.37 Na OH A:Tyr117 2.36 Na O A:Ile127 4.23 Na O A:Phe130 4.29 Na CB A:Phe130 4.33 Na C A:Phe130 4.86 Na O A:Gly131 5.00 Na CD1 B:Tyr117 4.06 Na CE1 B:Tyr117 4.10 Na O B:Phe130 4.88 Na CB B:Phe130 4.48 Na O B:Gly131 3.99 Na OG B:Ser133 4.04 Na O A:Hoh303 4.45 Na O A:Hoh310 4.45 Na O A:Hoh546 2.21 Na O B:Hoh266 2.62 Na O B:Hoh267 2.08 Na O B:Hoh270 2.18 Na O B:Hoh275 4.40 Na O B:Hoh277 4.75 interactive model: