Sodium in PDB 6d2s: Mycobacterium Tuberculosis Transcriptional Regulator

The structure of Mycobacterium Tuberculosis Transcriptional Regulator, PDB code: 6d2s was solved by S.Tang, J.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.10 / 1.82
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.999, 81.724, 95.365, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.9

The structure of Mycobacterium Tuberculosis Transcriptional Regulator also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Transcriptional Regulator (pdb code 6d2s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mycobacterium Tuberculosis Transcriptional Regulator, PDB code: 6d2s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Transcriptional Regulator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Tuberculosis Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:43.7 occ:1.00 OD2 A:ASP171 2.3 39.8 1.0 O A:HOH725 3.0 53.1 1.0 O A:HOH736 3.1 47.0 1.0 CG A:ASP171 3.1 34.4 1.0 OD1 A:ASP171 3.3 39.2 1.0 CB A:ASP171 4.6 21.8 1.0 O A:HOH720 4.8 25.5 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Transcriptional Regulator


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Tuberculosis Transcriptional Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:18.9 occ:1.00 O A:HOH703 2.1 28.7 1.0 O A:SER350 2.2 40.9 1.0 O A:HOH660 2.4 36.7 1.0 O A:HOH643 2.5 25.2 1.0 OD1 A:ASN166 2.6 39.4 1.0 C A:SER350 3.4 46.3 1.0 CG A:ASN166 3.8 36.0 1.0 CA A:ALA351 4.1 40.7 1.0 N A:ALA351 4.1 44.1 1.0 CA A:ASN166 4.4 13.2 1.0 O A:HOH768 4.4 43.4 1.0 O A:TYR163 4.4 15.6 1.0 CA A:SER350 4.4 41.9 1.0 O A:HOH652 4.4 44.0 1.0 C A:ALA351 4.4 36.4 1.0 CB A:ASN166 4.4 15.8 1.0 CE1 A:TYR163 4.6 20.8 1.0 O A:ALA351 4.6 48.6 1.0 CZ A:TYR163 4.7 19.4 1.0 OH A:TYR163 4.8 20.8 1.0 ND2 A:ASN166 4.9 40.9 1.0 O A:HOH638 4.9 41.1 1.0 N A:ASN166 5.0 13.2 1.0 O A:THR352 5.0 51.6 1.0

S.Tang, N.D.Hicks, Y.S.Cheng, A.Silva, S.M.Fortune, J.C.Sacchettini. Structural and Functional Insight Into the Mycobacterium Tuberculosis Protein Prpr Reveals A Novel Type of Transcription Factor. Nucleic Acids Res. V. 47 9934 2019.
ISSN: ESSN 1362-4962
PubMed: 31504787
DOI: 10.1093/NAR/GKZ724