Sodium in PDB 3nw8: Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH

The structure of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH, PDB code: 3nw8 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)	48.69 / 2.76
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	117.985, 117.985, 321.537, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.2

The structure of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH (pdb code 3nw8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH, PDB code: 3nw8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-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, Y179S Mutant, High-pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:60.0 occ:1.00 O B:ASP226 3.6 50.6 1.0 C B:ASP226 4.3 50.6 1.0 CD1 B:PHE223 4.7 64.0 1.0 CG B:PHE223 4.8 64.0 1.0 C B:ASP227 4.9 57.7 1.0 N B:ASP227 4.9 57.7 1.0 CA B:ASP227 5.0 57.7 1.0

Sodium binding site 2 out of 4 in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1 b:50.7 occ:1.00 NH2 C:ARG304 3.7 68.7 1.0 NH1 C:ARG304 4.2 68.7 1.0 OG1 C:THR341 4.3 35.1 1.0 CZ C:ARG304 4.4 68.7 1.0 N C:GLY324 4.4 62.3 1.0 CB C:PRO339 4.7 44.3 1.0 C C:THR340 4.7 47.0 1.0 O C:THR340 4.8 47.0 1.0 CA C:GLY324 4.8 62.3 1.0 O C:PRO339 4.9 44.3 1.0 C C:PRO339 4.9 44.3 1.0 N C:THR341 5.0 35.1 1.0

Sodium binding site 3 out of 4 in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Na4 b:87.5 occ:1.00 O C:ALA278 3.6 48.8 1.0 CB C:LYS158 3.6 38.1 1.0 O C:PHE159 3.7 21.3 1.0 CB C:ASP277 3.7 39.0 1.0 N C:PHE159 3.7 21.3 1.0 O C:HOH741 3.7 39.8 1.0 CE C:LYS160 3.7 43.6 1.0 CD C:LYS160 3.8 43.6 1.0 CG C:ASP277 3.9 39.0 1.0 N C:ALA278 4.0 48.8 1.0 OD1 C:ASP277 4.0 39.0 1.0 C C:PHE159 4.1 21.3 1.0 C C:LYS158 4.1 38.1 1.0 CA C:LYS158 4.1 38.1 1.0 CA C:ASP277 4.2 39.0 1.0 O C:HOH736 4.3 15.9 1.0 CA C:PHE159 4.4 21.3 1.0 CG C:LYS158 4.4 38.1 1.0 C C:ASP277 4.5 39.0 1.0 C C:ALA278 4.5 48.8 1.0 OD2 C:ASP277 4.6 39.0 1.0 N C:LYS160 4.9 43.6 1.0 CA C:ALA278 4.9 48.8 1.0 CD C:LYS158 4.9 38.1 1.0 O C:LYS158 4.9 38.1 1.0

Sodium binding site 4 out of 4 in the Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, High-pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Na3 b:38.6 occ:1.00 O D:MET366 3.3 45.6 1.0 OAF D:MRY2000 3.4 80.7 1.0 CAE D:MRY2000 3.7 80.7 1.0 SG D:CYS412 3.7 47.6 1.0 CB D:CYS364 3.8 52.8 1.0 ND2 D:ASN153 3.9 38.6 1.0 CB D:CYS412 4.0 47.6 1.0 CA D:THR367 4.1 27.1 1.0 OG1 D:THR367 4.2 27.1 1.0 C D:MET366 4.3 45.6 1.0 SG D:CYS364 4.5 52.8 1.0 OD2 D:ASP416 4.5 82.8 1.0 CAA D:MRY2000 4.6 80.7 1.0 CB D:THR367 4.6 27.1 1.0 CAG D:MRY2000 4.6 80.7 1.0 CG2 D:THR367 4.7 27.1 1.0 O D:CYS364 4.7 52.8 1.0 N D:THR367 4.7 27.1 1.0 CAC D:MRY2000 4.7 80.7 1.0 CA D:CYS364 4.9 52.8 1.0 N D:LYS368 4.9 43.8 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