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

The structure of Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-I Crystal, PDB code: 5vpe 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)	47.31 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.479, 90.755, 105.618, 90.00, 117.93, 90.00
R / Rfree (%)	21.8 / 25.4

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

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-I Crystal (pdb code 5vpe). 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 Complex with Cognate Dna, Type-I Crystal, PDB code: 5vpe:
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 Complex with Cognate Dna, Type-I 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-I Crystal within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:64.5 occ:1.00 HB3 C:ASN174 3.0 31.4 1.0 HG3 C:LYS171 3.0 32.1 1.0 HG3 C:ARG175 3.2 32.0 1.0 HA C:LYS171 3.5 31.6 1.0 CB C:ASN174 3.9 26.5 1.0 CG C:LYS171 3.9 27.1 1.0 O C:LYS171 4.0 25.6 1.0 HB2 C:ASN174 4.0 31.4 1.0 CG C:ARG175 4.0 26.6 1.0 HG2 C:ARG175 4.1 32.0 1.0 H C:ARG175 4.3 29.6 1.0 HG2 C:LYS171 4.3 32.1 1.0 CA C:LYS171 4.3 26.6 1.0 OE1 C:GLU178 4.3 57.6 1.0 N C:ARG175 4.4 25.0 1.0 OD1 C:ASN174 4.5 49.1 1.0 HE3 C:LYS171 4.5 46.1 1.0 CB C:LYS171 4.5 27.1 1.0 CG C:ASN174 4.6 37.7 1.0 C C:LYS171 4.6 25.8 1.0 HB2 C:LYS171 4.6 32.1 1.0 OE2 C:GLU178 4.6 58.2 1.0 HD2 C:ARG175 4.6 39.2 1.0 HA C:ARG175 4.7 29.1 1.0 C C:ASN174 4.7 25.2 1.0 CD C:GLU178 4.8 59.5 1.0 CD C:ARG175 4.9 32.6 1.0 CA C:ASN174 4.9 25.7 1.0 HD2 C:LYS171 4.9 32.9 1.0 CD C:LYS171 4.9 27.8 1.0 CA C:ARG175 5.0 24.6 1.0

Sodium binding site 2 out of 3 in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-I 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 Complex with Cognate Dna, Type-I Crystal within 5.0Å range: probe atom residue distance (Å) B Occ G:Na102 b:55.7 occ:1.00 HH22 D:ARG286 3.3 29.8 0.6 HB2 D:SER283 3.5 15.5 0.7 H3' G:DA9 3.6 23.0 1.0 HB3 D:SER283 3.7 15.5 0.3 HB2 D:SER283 3.7 15.5 0.3 O D:HOH531 3.8 48.8 1.0 OG D:SER283 3.9 13.8 0.7 HH21 D:ARG286 3.9 29.8 0.6 NH2 D:ARG286 3.9 24.7 0.6 OP2 G:DC10 4.0 18.6 1.0 CB D:SER283 4.1 13.2 0.7 CB D:SER283 4.1 13.2 0.3 OP1 G:DA9 4.4 27.5 1.0 H5'' G:DA9 4.5 27.2 1.0 C3' G:DA9 4.5 19.4 1.0 HB3 D:SER283 4.6 15.5 0.7 O5' G:DA9 4.6 24.9 1.0 HG D:SER283 4.6 16.1 0.7 P G:DC10 4.8 19.1 1.0 O3' G:DA9 4.8 19.2 1.0 P G:DA9 4.9 25.5 1.0 OG D:SER283 4.9 13.3 0.3 O D:HOH523 4.9 37.4 1.0 OP2 G:DA9 4.9 26.1 1.0 OP1 G:DC10 5.0 26.7 1.0 C5' G:DA9 5.0 22.6 1.0

Sodium binding site 3 out of 3 in the Transcription Factor Fosb/Jund Bzip Domain in Complex with Cognate Dna, Type-I 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 Complex with Cognate Dna, Type-I Crystal within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:58.6 occ:1.00 H5'' E:DT11 3.3 27.1 1.0 HD3 B:ARG275 3.6 29.8 1.0 NE B:ARG275 3.8 27.1 1.0 CZ B:ARG275 3.9 32.8 1.0 CD B:ARG275 4.1 25.2 1.0 HE B:ARG275 4.1 32.6 1.0 NH1 B:ARG275 4.1 34.6 1.0 HD2 B:ARG275 4.1 29.8 1.0 HH11 B:ARG275 4.2 41.6 1.0 C5' E:DT11 4.3 22.9 1.0 OP1 E:DC12 4.3 32.3 1.0 OP1 E:DT11 4.4 24.4 1.0 O3' E:DT11 4.4 24.3 1.0 NH2 B:ARG275 4.4 25.3 1.0 HH12 B:ARG275 4.5 41.6 1.0 HH21 B:ARG275 4.6 30.2 1.0 HH22 B:ARG275 4.7 30.2 1.0 H5' E:DT11 4.8 27.1 1.0 H3' E:DT11 4.8 26.8 1.0 P E:DC12 4.8 28.5 1.0 H4' E:DT11 4.9 26.5 1.0 O5' E:DT11 4.9 22.1 1.0 C4' E:DT11 4.9 22.4 1.0 C3' E:DT11 4.9 22.6 1.0 HH21 B:ARG268 5.0 91.0 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