Sodium in the structure of Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH (pdb 3nwf)

The binding sites of Sodium atom in the structure of Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH (pdb code 3nwf). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3nwf structure was solved by S.D.STAMPFER, H.LOU, G.H.COHEN, R.J.EISENBERG, E.E.HELDWEIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 41.5-3.0 Space group P3 a (A) 117.802 b (A) 117.802 c (A) 318.324 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.7 Rfree (%) 24.9 Sodium Binding Sites: Sodium binding site 1 out of 1 in 3nwf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3nwf. 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: B: Lys235, B: Pro236, B: Asn238, conact list: Atom Atom Distance (A) Na CB B:Lys235 4.36 Na CD B:Lys235 4.81 Na C B:Lys235 4.83 Na CG B:Lys235 4.70 Na O B:Pro236 3.20 Na N B:Pro236 4.57 Na CB B:Pro236 4.82 Na CD B:Pro236 4.61 Na C B:Pro236 4.34 Na CA B:Pro236 4.87 Na OD1 B:Asn238 4.56 interactive model: