Sodium in PDB 4zxs: Hsv-1 Nuclear Egress Complex

The structure of Hsv-1 Nuclear Egress Complex, PDB code: 4zxs was solved by J.M.Bigalke, E.E.Heldwein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.86 / 2.77
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	110.529, 110.529, 155.850, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.5

The structure of Hsv-1 Nuclear Egress Complex also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Hsv-1 Nuclear Egress Complex (pdb code 4zxs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hsv-1 Nuclear Egress Complex, PDB code: 4zxs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hsv-1 Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hsv-1 Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:49.0 occ:1.00 O B:ALA103 3.2 45.9 1.0 O B:TYR228 3.2 52.4 1.0 O B:HOH521 3.2 55.3 1.0 O B:VAL102 3.2 44.8 1.0 C B:ALA103 3.4 43.7 1.0 N B:ASP232 3.5 38.2 1.0 O B:ASN105 3.5 37.6 1.0 CA B:ALA103 3.6 24.5 1.0 CB B:ILE231 3.7 31.5 1.0 CG2 B:ILE231 3.8 30.9 1.0 CB B:ASP232 3.8 44.1 1.0 CA B:ASP232 3.9 40.8 1.0 N B:ASN105 3.9 31.8 1.0 C B:VAL102 4.0 38.1 1.0 C B:TYR228 4.0 58.3 1.0 C B:ILE231 4.1 43.1 1.0 N B:ASP104 4.1 34.7 1.0 CA B:TYR228 4.2 54.1 1.0 N B:ALA103 4.2 34.3 1.0 C B:ASN105 4.4 49.1 1.0 CB B:TYR228 4.4 45.2 1.0 CA B:ILE231 4.5 49.2 1.0 CA B:ASN105 4.5 34.1 1.0 CG B:ASP232 4.6 59.6 1.0 OD1 B:ASP232 4.6 70.8 1.0 OG1 B:THR101 4.7 23.7 1.0 C B:ASP104 4.7 36.9 1.0 CB B:ASN105 4.7 49.6 1.0 CA B:ASP104 4.7 39.2 1.0 CG1 B:ILE231 4.8 30.5 1.0 CB B:THR101 4.8 37.1 1.0 O B:ILE231 4.9 61.8 1.0 CB B:ALA103 4.9 34.6 1.0 CD1 B:ILE231 4.9 46.5 1.0 N B:ILE231 5.0 41.6 1.0

Sodium binding site 2 out of 2 in the Hsv-1 Nuclear Egress Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hsv-1 Nuclear Egress Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:47.2 occ:1.00 O D:PHE219 2.7 47.5 1.0 N D:PHE252 2.7 39.8 1.0 O D:GLY221 2.8 59.0 1.0 CB D:PHE252 3.5 45.7 1.0 CA D:PHE252 3.6 47.6 1.0 C D:THR251 3.6 40.8 1.0 C D:PHE219 3.7 50.5 1.0 CA D:THR251 3.7 42.1 1.0 O D:PHE252 3.7 42.9 1.0 CG2 D:THR251 3.8 40.5 1.0 CD2 D:PHE252 3.9 45.2 1.0 C D:GLY221 3.9 59.4 1.0 CB D:PHE219 4.1 47.5 1.0 CG D:PHE252 4.1 49.2 1.0 C D:PHE252 4.1 37.6 1.0 O D:PRO220 4.2 62.8 1.0 C D:PRO220 4.3 57.8 1.0 CA D:PHE219 4.3 43.6 1.0 CB D:THR251 4.3 42.1 1.0 O D:HOH519 4.4 45.2 1.0 O D:SER250 4.5 54.3 1.0 N D:GLY221 4.5 55.5 1.0 N D:PRO220 4.6 43.2 1.0 N D:PHE219 4.6 54.9 1.0 CA D:THR222 4.8 52.4 1.0 N D:THR222 4.8 65.1 1.0 CA D:PRO220 4.8 46.1 1.0 O D:THR251 4.8 40.8 1.0 N D:THR251 4.8 49.2 1.0 CA D:GLY221 4.8 58.5 1.0 C D:THR222 5.0 50.6 1.0

J.M.Bigalke, E.E.Heldwein. Structural Basis of Membrane Budding By the Nuclear Egress Complex of Herpesviruses. Embo J. V. 34 2921 2015.
ISSN: ESSN 1460-2075
PubMed: 26511020
DOI: 10.15252/EMBJ.201592359