Sodium in PDB 6z74: Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum

The structure of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum, PDB code: 6z74 was solved by S.Morera, V.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.170, 113.660, 130.520, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.5

The structure of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum (pdb code 6z74). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum, PDB code: 6z74:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:62.4 occ:1.00 NH1 D:ARG31 3.7 46.2 1.0 O D:HOH409 4.4 58.4 1.0 CZ D:ARG31 4.6 63.0 1.0 NH2 D:ARG31 4.7 50.6 1.0

Sodium binding site 2 out of 2 in the Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Transcriptional Repressor ATU1419 (Vanr) in Complex with A Fortuitous Citrate From Agrobacterium Fabrum within 5.0Å range: probe atom residue distance (Å) B Occ D:Na304 b:36.6 occ:1.00 O D:HOH448 3.1 53.9 1.0 N D:GLU34 3.2 43.0 1.0 CA D:PHE33 3.6 43.7 1.0 CA D:GLY68 3.7 40.4 1.0 CE1 D:PHE69 3.9 47.2 1.0 C D:PHE33 3.9 46.7 1.0 N D:GLY68 4.0 42.3 1.0 CB D:GLU34 4.2 46.0 1.0 CD1 D:PHE69 4.2 46.8 1.0 CB D:PHE33 4.2 44.6 1.0 CG D:GLU34 4.2 57.7 1.0 CA D:GLU34 4.3 44.4 1.0 CD1 D:PHE33 4.3 47.8 1.0 O D:LEU32 4.5 50.8 1.0 OE1 D:GLU34 4.6 67.8 1.0 C D:GLY68 4.7 45.8 1.0 CG D:PHE33 4.7 45.5 1.0 CD1 D:LEU52 4.7 47.4 1.0 N D:PHE33 4.8 45.3 1.0 CD D:GLU34 4.9 75.7 1.0

A.Vigouroux, T.Meyer, A.Naretto, P.Legrand, M.Aumont-Nicaise, A.Di Cicco, S.Renoud, J.Dore, D.Levy, L.Vial, C.Lavire, S.Morera. Characterization of the First Tetrameric Transcription Factor of the Gntr Superfamily with Allosteric Regulation From the Bacterial Pathogen Agrobacterium Fabrum Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962