Chlorine in PDB 3nwd: Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, Low-pH

The structure of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, Low-pH, PDB code: 3nwd 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)	48.56 / 2.88
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	117.757, 117.757, 318.560, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 28.3

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

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, Low-pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:78.4 occ:1.00 ND2 A:ASN511 3.4 37.6 1.0 CB A:ASN511 3.4 37.6 1.0 OG A:SER387 3.9 32.0 1.0 CG A:ASN511 3.9 37.6 1.0 CD2 A:HIS512 4.3 76.4 1.0 OG1 A:THR394 4.4 75.8 1.0 CD A:ARG385 4.4 67.7 1.0 OH A:TYR142 4.4 74.0 1.0 CG2 A:THR394 4.7 75.8 1.0 CA A:ASN511 4.7 37.6 1.0 NE2 A:HIS512 4.8 76.4 1.0 N A:HIS512 4.8 76.4 1.0 CB A:SER387 4.9 32.0 1.0 C A:ASN511 4.9 37.6 1.0 CB A:ARG385 4.9 67.7 1.0 NE A:ARG385 5.0 67.7 1.0 NE A:ARG515 5.0 74.8 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Glycoprotein B From Herpes Simplex Virus Type 1, Y179S Mutant, Low-pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1 b:59.1 occ:1.00 ND2 D:ASN153 3.2 36.6 1.0 N D:CYS364 3.9 54.1 1.0 O D:CYS364 4.0 54.1 1.0 CA D:VAL363 4.1 54.2 1.0 CG D:ASN153 4.3 36.6 1.0 O D:SER362 4.4 71.3 1.0 C D:VAL363 4.5 54.2 1.0 O D:ALA155 4.6 62.7 1.0 CB D:VAL363 4.7 54.2 1.0 CA D:CYS364 4.8 54.1 1.0 OD1 D:ASN153 4.8 36.6 1.0 C D:CYS364 4.8 54.1 1.0 CA D:TYR157 4.9 58.8 1.0 CG1 D:VAL363 4.9 54.2 1.0 OH D:TYR284 5.0 67.8 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