Sodium in PDB 4lqk: Structure of the Vaccinia Virus Nf- B Antagonist A46

The structure of Structure of the Vaccinia Virus Nf- B Antagonist A46, PDB code: 4lqk was solved by I.Grishkovskaya, S.Fedosyuk, T.Skern, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.46 / 1.99
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.114, 107.633, 137.899, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 21.9

The structure of Structure of the Vaccinia Virus Nf- B Antagonist A46 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Structure of the Vaccinia Virus Nf- B Antagonist A46 (pdb code 4lqk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Vaccinia Virus Nf- B Antagonist A46, PDB code: 4lqk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Vaccinia Virus Nf- B Antagonist A46


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Vaccinia Virus Nf- B Antagonist A46 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:17.5 occ:1.00 OG D:SER205 3.1 20.5 1.0 O D:HOH407 3.3 26.3 1.0 O D:HOH416 3.6 37.1 1.0 C D:SER205 3.8 23.6 1.0 N D:LYS206 3.8 23.8 1.0 O D:SER205 3.8 22.5 1.0 CG D:ARG209 3.8 29.9 1.0 CB D:SER205 3.9 21.6 1.0 CA D:LYS206 3.9 25.9 1.0 NH1 D:ARG209 4.0 30.2 1.0 CD2 D:HIS211 4.1 38.9 1.0 CG D:LYS206 4.1 28.5 1.0 O D:HOH409 4.2 23.3 0.5 CB D:ARG209 4.3 29.1 1.0 CA D:SER205 4.5 22.2 1.0 NE2 D:HIS211 4.5 39.4 1.0 CB D:LYS206 4.7 26.2 1.0 CD D:ARG209 4.8 30.6 1.0 CZ D:ARG209 5.0 30.7 0.8

Sodium binding site 2 out of 2 in the Structure of the Vaccinia Virus Nf- B Antagonist A46


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Vaccinia Virus Nf- B Antagonist A46 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:13.3 occ:1.00 OG B:SER205 3.1 17.5 1.0 O B:HOH402 3.2 18.5 1.0 C B:SER205 3.6 17.5 1.0 O B:SER205 3.6 16.3 1.0 N B:LYS206 3.6 17.8 1.0 CA B:LYS206 3.8 20.0 1.0 CB B:SER205 3.8 17.1 1.0 CG B:ARG209 3.8 21.1 1.0 CG B:LYS206 3.9 24.1 1.0 CD2 B:HIS211 4.1 28.4 1.0 O B:HOH412 4.1 13.0 0.4 CB B:ARG209 4.1 20.5 1.0 NH1 B:ARG209 4.2 22.9 1.0 O B:HOH408 4.2 24.6 1.0 CA B:SER205 4.3 16.8 1.0 NE2 B:HIS211 4.5 30.0 1.0 CB B:LYS206 4.5 21.2 1.0 CD B:ARG209 4.9 22.1 0.9 C B:LYS206 5.0 19.9 1.0

S.Fedosyuk, I.Grishkovskaya, E.De Almeida Ribeiro, T.Skern. Characterization and Structure of the Vaccinia Virus Nf-Kappa B Antagonist A46. J.Biol.Chem. V. 289 3749 2014.
ISSN: ISSN 0021-9258
PubMed: 24356965
DOI: 10.1074/JBC.M113.512756