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

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

Resolution Low / High (Å)	44.04 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.177, 49.949, 97.746, 90.00, 122.94, 90.00
R / Rfree (%)	25.1 / 28.9

The structure of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- II 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- II Crystal (pdb code 5vpc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- II Crystal, PDB code: 5vpc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, 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 Its Oxidized Form, Type- II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:46.6 occ:1.00 O B:HOH515 2.7 47.2 1.0 HH21 B:ARG318 2.8 53.8 1.0 OE1 A:GLU200 2.9 81.2 1.0 NH2 B:ARG318 3.1 44.3 1.0 HH22 B:ARG318 3.3 53.8 1.0 OE2 A:GLU200 3.4 54.1 1.0 HD21 A:LEU197 3.6 51.6 1.0 CD A:GLU200 3.6 51.0 1.0 HD23 A:LEU197 3.7 51.6 1.0 CZ B:ARG318 4.0 42.0 1.0 CD2 A:LEU197 4.0 42.6 1.0 HE B:ARG318 4.0 74.3 1.0 HD22 A:LEU197 4.3 51.6 1.0 NE B:ARG318 4.3 61.5 1.0 HB1 B:ALA314 4.7 35.9 1.0 HB3 B:ALA314 4.9 35.9 1.0 NH1 B:ARG318 4.9 65.8 1.0

Sodium binding site 2 out of 3 in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- II 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- II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:52.1 occ:1.00 HB2 A:GLU198 3.1 51.5 1.0 HA A:ALA195 3.5 73.5 1.0 OE1 A:GLU198 3.5 49.9 1.0 O A:ALA195 3.6 52.5 1.0 HB1 A:ALA195 3.6 55.7 1.0 HB3 A:GLU198 3.8 51.5 1.0 CB A:GLU198 3.9 42.4 1.0 HB2 A:SER199 4.0 60.2 1.0 H A:SER199 4.0 56.0 1.0 CA A:ALA195 4.1 60.8 1.0 C A:ALA195 4.2 62.7 1.0 CB A:ALA195 4.3 46.0 1.0 N A:SER199 4.3 46.2 1.0 CD A:GLU198 4.5 52.6 1.0 HB2 A:ALA195 4.6 55.7 1.0 HA A:SER199 4.7 81.2 1.0 C A:GLU198 4.8 57.2 1.0 CG A:GLU198 4.8 54.8 1.0 CB A:SER199 4.8 49.7 1.0 CA A:SER199 4.9 67.2 1.0 CA A:GLU198 4.9 56.8 1.0

Sodium binding site 3 out of 3 in the Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- II Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Transcription Factor Fosb/Jund Bzip Domain in Its Oxidized Form, Type- II Crystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:47.9 occ:1.00 HB3 B:ARG318 2.8 29.7 1.0 HA B:GLU319 3.0 46.4 1.0 N B:GLU319 3.4 37.9 1.0 C B:ARG318 3.4 29.6 1.0 O B:ARG318 3.5 25.8 1.0 CA B:GLU319 3.6 38.2 1.0 CB B:ARG318 3.6 24.3 1.0 H B:GLU319 3.7 46.1 1.0 HB2 B:ARG318 3.8 29.7 1.0 HB2 B:ALA322 3.9 16.9 1.0 HB2 B:GLU319 4.1 26.6 1.0 O B:HOH501 4.1 63.0 1.0 CA B:ARG318 4.2 39.4 1.0 O B:HOH503 4.2 31.7 1.0 HD2 B:ARG318 4.3 51.6 1.0 HB3 B:ALA322 4.3 16.9 1.0 CB B:GLU319 4.4 21.7 1.0 HG3 B:GLU319 4.4 79.2 1.0 CB B:ALA322 4.5 13.7 1.0 HH11 B:ARG318 4.6 79.5 1.0 HA B:ARG318 4.7 47.9 1.0 O B:SER315 4.7 26.2 1.0 CG B:ARG318 4.8 29.4 1.0 C B:GLU319 4.9 34.8 1.0 HB1 B:ALA322 4.9 16.9 1.0 CG B:GLU319 5.0 65.5 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