Sodium in PDB 5vpd: Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal

The structure of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal, PDB code: 5vpd was solved by Z.Yin, M.Machius, G.Rudenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.72 / 2.79
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.008, 98.051, 50.251, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 30

The structure of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal (pdb code 5vpd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal, PDB code: 5vpd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:37.6 occ:1.00 HB3 A:LYS206 2.7 52.5 1.0 HB2 A:ARG210 3.4 86.0 1.0 CB A:LYS206 3.6 43.8 1.0 O A:LYS206 3.6 53.8 1.0 HD2 A:ARG210 3.6 0.5 1.0 C A:LYS206 3.7 55.6 1.0 HB2 A:LYS206 3.8 52.5 1.0 HA A:GLU207 3.8 40.2 1.0 HD3 A:ARG210 4.0 0.5 1.0 N A:GLU207 4.1 42.7 1.0 HB3 A:ARG210 4.2 86.0 1.0 CA A:LYS206 4.2 52.0 1.0 CB A:ARG210 4.2 71.7 1.0 CD A:ARG210 4.2 87.9 1.0 HD2 A:LYS206 4.5 88.6 1.0 HA A:LYS206 4.5 62.4 1.0 CA A:GLU207 4.5 33.5 1.0 OE1 A:GLU207 4.5 41.5 1.0 H A:GLU207 4.6 51.3 1.0 HG3 A:LYS206 4.6 68.6 1.0 CG A:LYS206 4.6 57.1 1.0 OE2 A:GLU203 4.8 74.3 1.0 H A:ARG210 4.8 40.8 1.0 CG A:ARG210 4.8 83.3 1.0

Sodium binding site 2 out of 2 in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- III Crystal within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:64.3 occ:1.00 HH22 D:ARG318 3.1 99.2 1.0 HH12 D:ARG318 3.6 0.4 1.0 NH2 D:ARG318 3.6 82.7 1.0 OE1 C:GLU200 3.6 45.1 1.0 NH1 D:ARG318 4.0 94.5 1.0 HH21 D:ARG318 4.0 99.2 1.0 CZ D:ARG318 4.1 66.8 1.0 OE2 C:GLU200 4.1 43.0 1.0 HD21 C:LEU197 4.1 36.0 1.0 HD23 C:LEU197 4.3 36.0 1.0 CD C:GLU200 4.3 41.5 1.0 HH11 D:ARG318 4.6 0.4 1.0 CD2 C:LEU197 4.7 30.0 1.0

Z.Yin, M.Machius, E.J.Nestler, G.Rudenko. Activator Protein-1: Redox Switch Controlling Structure and Dna-Binding. Nucleic Acids Res. V. 45 11425 2017.
ISSN: ESSN 1362-4962
PubMed: 28981703
DOI: 10.1093/NAR/GKX795