Sodium in PDB 5vpf: Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal

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

Resolution Low / High (Å)	48.59 / 2.69
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.637, 119.637, 249.970, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.8

The structure of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II Crystal (pdb code 5vpf). 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 in Complex with Cognate Dna, Type-II Crystal, PDB code: 5vpf:

Sodium binding site 1 out of 1 in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-II 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 Complex with Cognate Dna, Type-II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:35.9 occ:1.00 HH12 B:ARG286 3.3 33.0 0.5 OG B:SER283 3.5 32.8 1.0 HB2 B:SER283 3.7 39.4 1.0 H3' E:DA9 4.0 22.7 1.0 O1 B:EDO401 4.1 37.3 1.0 CB B:SER283 4.1 32.8 1.0 HG B:SER283 4.1 39.4 1.0 HO1 B:EDO401 4.2 44.8 1.0 NH1 B:ARG286 4.2 27.5 0.5 OP2 E:DC10 4.3 25.8 1.0 HH22 B:ARG286 4.4 19.3 0.5 H11 B:EDO401 4.5 45.2 1.0 O2 B:EDO401 4.5 58.1 1.0 HH11 B:ARG286 4.6 33.0 0.5 OP1 E:DA9 4.7 22.1 1.0 HB3 B:SER283 4.8 39.4 1.0 C1 B:EDO401 4.8 37.6 1.0 HA B:SER283 4.8 18.6 1.0 O5' E:DA9 4.9 31.3 1.0 C3' E:DA9 5.0 18.9 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