Sodium in PDB 2gum: Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I

The structure of Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I, PDB code: 2gum was solved by E.E.Heldwein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	84.959, 100.039, 100.133, 67.04, 77.99, 70.31
R / Rfree (%)	24.8 / 27.5

The binding sites of Sodium atom in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I (pdb code 2gum). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I, PDB code: 2gum:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na731 b:42.0 occ:1.00 O A:HOH757 2.8 41.8 1.0 OD1 A:ASN540 2.9 38.2 1.0 NE2 A:GLN129 3.2 47.2 1.0 ND2 A:ASN540 3.6 37.3 1.0 CG A:ASN540 3.6 37.3 1.0 O A:HOH788 3.6 47.1 1.0 CB A:PHE127 3.7 35.9 1.0 NH1 A:ARG543 3.9 51.5 1.0 NH2 A:ARG543 4.0 51.0 1.0 CD1 A:PHE127 4.0 38.4 1.0 CZ A:ARG543 4.1 49.9 1.0 CD1 A:LEU536 4.2 27.8 1.0 CG A:PHE127 4.2 37.0 1.0 CD A:GLN129 4.4 49.5 1.0 O A:PHE127 4.6 34.5 1.0 N A:PHE127 4.6 36.0 1.0 CA A:PHE127 4.7 35.6 1.0 NH2 C:ARG661 4.7 66.1 1.0 OE1 A:GLN129 4.7 49.9 1.0 CG A:LEU536 4.8 32.4 1.0 CD2 A:LEU536 4.9 32.1 1.0 C A:PHE127 5.0 32.3 1.0 CB A:ASN540 5.0 35.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I within 5.0Å range: probe atom residue distance (Å) B Occ B:Na731 b:50.7 occ:1.00 O B:HOH741 2.7 32.9 1.0 OD1 B:ASN540 2.7 35.2 1.0 NE2 B:GLN129 3.3 44.7 1.0 CG B:ASN540 3.5 35.5 1.0 ND2 B:ASN540 3.6 36.1 1.0 NH2 B:ARG543 3.7 51.3 1.0 CB B:PHE127 3.7 38.1 1.0 CD1 B:PHE127 4.0 37.9 1.0 CZ B:ARG543 4.1 50.6 1.0 NH1 B:ARG543 4.2 50.3 1.0 CD1 B:LEU536 4.2 33.5 1.0 CG B:PHE127 4.3 38.5 1.0 CD B:GLN129 4.4 45.2 1.0 OE1 B:GLN129 4.7 47.7 1.0 O B:PHE127 4.8 37.5 1.0 CA B:PHE127 4.8 37.2 1.0 CG B:LEU536 4.8 37.9 1.0 N B:PHE127 4.8 37.6 1.0 CB B:ASN540 4.8 34.1 1.0 NH2 A:ARG661 4.9 66.7 1.0 CD2 B:LEU536 4.9 36.0 1.0 NE B:ARG543 5.0 51.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I within 5.0Å range: probe atom residue distance (Å) B Occ B:Na732 b:52.8 occ:1.00 O B:HOH763 2.3 34.2 1.0 O B:HOH748 2.9 33.2 1.0 O B:ILE671 3.2 27.3 1.0 N B:LEU673 3.4 34.2 1.0 CA B:ASP672 3.4 34.0 1.0 NH1 C:ARG131 3.6 28.2 1.0 CD1 C:TRP528 3.7 30.1 1.0 C B:ASP672 3.8 36.4 1.0 NE1 C:TRP528 3.9 27.5 1.0 C B:ILE671 4.0 27.9 1.0 OD1 B:ASP672 4.1 47.1 1.0 N B:ASP672 4.2 30.8 1.0 O B:LEU673 4.3 38.9 1.0 CA B:LEU673 4.4 34.6 1.0 CB B:LEU673 4.4 31.2 1.0 CB B:ASP672 4.4 39.2 1.0 O C:HOH757 4.5 38.3 1.0 CG C:GLN532 4.6 27.1 1.0 CG B:ASP672 4.7 44.3 1.0 C B:LEU673 4.7 36.1 1.0 O B:ASP672 4.8 36.3 1.0 CZ C:ARG131 4.9 31.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Extracellular Domain of Glycoprotein B From Herpes Simplex Virus Type I within 5.0Å range: probe atom residue distance (Å) B Occ C:Na731 b:44.9 occ:1.00 OD1 C:ASN540 2.7 30.0 1.0 O C:HOH745 2.8 24.0 1.0 NE2 C:GLN129 3.3 46.8 1.0 CG C:ASN540 3.5 30.1 1.0 ND2 C:ASN540 3.6 30.5 1.0 CB C:PHE127 3.6 31.6 1.0 O C:HOH810 3.9 40.8 1.0 CD1 C:PHE127 3.9 34.0 1.0 NH1 C:ARG543 4.1 55.0 1.0 CD1 C:LEU536 4.1 27.0 1.0 CG C:PHE127 4.2 33.2 1.0 NH2 C:ARG543 4.2 56.0 1.0 CD C:GLN129 4.4 48.0 1.0 CZ C:ARG543 4.4 55.8 1.0 OE1 C:GLN129 4.6 50.7 1.0 CG C:LEU536 4.6 27.8 1.0 O C:PHE127 4.6 30.8 1.0 CA C:PHE127 4.6 28.9 1.0 N C:PHE127 4.6 28.5 1.0 CD2 C:LEU536 4.7 28.1 1.0 CB C:ASN540 4.9 30.4 1.0 C C:PHE127 4.9 30.9 1.0

E.E.Heldwein, H.Lou, F.C.Bender, G.H.Cohen, R.J.Eisenberg, S.C.Harrison. Crystal Structure of Glycoprotein B From Herpes Simplex Virus 1. Science V. 313 217 2006.
ISSN: ISSN 0036-8075
PubMed: 16840698
DOI: 10.1126/SCIENCE.1126548