Sodium in PDB 3nwf: Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH

The structure of Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH, PDB code: 3nwf was solved by S.D.Stampfer, H.Lou, G.H.Cohen, R.J.Eisenberg, E.E.Heldwein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.54 / 3.00
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	117.802, 117.802, 318.324, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.9

The binding sites of Sodium atom in the Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH (pdb code 3nwf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH, PDB code: 3nwf:

Sodium binding site 1 out of 1 in the Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glycoprotein B From Herpes Simplex Virus Type 1, Low-pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:63.6 occ:1.00 O B:PRO236 3.2 71.5 1.0 C B:PRO236 4.3 71.5 1.0 CB B:LYS235 4.4 64.0 1.0 OD1 B:ASN238 4.6 27.5 1.0 N B:PRO236 4.6 71.5 1.0 CD B:PRO236 4.6 71.5 1.0 CG B:LYS235 4.7 64.0 1.0 CD B:LYS235 4.8 64.0 1.0 CB B:PRO236 4.8 71.5 1.0 C B:LYS235 4.8 64.0 1.0 CA B:PRO236 4.9 71.5 1.0

S.D.Stampfer, H.Lou, G.H.Cohen, R.J.Eisenberg, E.E.Heldwein. Structural Basis of Local, pH-Dependent Conformational Changes in Glycoprotein B From Herpes Simplex Virus Type 1. J.Virol. V. 84 12924 2010.
ISSN: ISSN 0022-538X
PubMed: 20943984
DOI: 10.1128/JVI.01750-10