Sodium in PDB 5vpa: Transcription Factor Fosb/Jund Bzip Domain

The structure of Transcription Factor Fosb/Jund Bzip Domain, PDB code: 5vpa 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)	34.20 / 2.83
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.605, 95.352, 98.200, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 28.3

The structure of Transcription Factor Fosb/Jund Bzip Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Transcription Factor Fosb/Jund Bzip Domain (pdb code 5vpa). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Transcription Factor Fosb/Jund Bzip Domain, PDB code: 5vpa:

Sodium binding site 1 out of 1 in the Transcription Factor Fosb/Jund Bzip Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:33.5 occ:1.00 OE1 B:GLU309 3.3 96.5 1.0 HG B:LEU310 3.3 35.6 1.0 HB3 B:GLU309 3.4 74.8 1.0 HD21 B:LEU310 3.4 14.6 1.0 HA B:GLN306 3.5 44.0 1.0 HG2 B:GLN306 3.5 78.6 1.0 HB3 B:GLN306 3.5 0.6 1.0 HD23 B:LEU310 3.7 14.6 1.0 CD B:GLU309 3.7 74.7 1.0 HG2 B:GLU309 3.8 92.9 1.0 O B:GLN306 3.9 14.1 1.0 CD2 B:LEU310 3.9 13.9 1.0 CG B:LEU310 4.1 29.3 1.0 CG B:GLU309 4.1 77.0 1.0 CB B:GLN306 4.1 85.2 1.0 CA B:GLN306 4.2 36.3 1.0 CB B:GLU309 4.2 62.0 1.0 CG B:GLN306 4.3 65.1 1.0 HD11 B:LEU310 4.4 49.7 1.0 OE2 B:GLU309 4.4 47.6 1.0 C B:GLN306 4.5 34.2 1.0 H B:LEU310 4.7 38.5 1.0 HB2 B:GLU309 4.8 74.8 1.0 HE21 B:GLN306 4.8 0.0 1.0 N B:LEU310 4.8 31.8 1.0 CD1 B:LEU310 4.8 41.1 1.0 HD22 B:LEU310 4.8 14.6 1.0 HG3 B:GLN306 4.9 78.6 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