Sodium in PDB 6b5e: Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose

All present enzymatic activity of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose:
2.7.7.24;

The structure of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose, PDB code: 6b5e was solved by H.A.Brown, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.323, 111.264, 290.363, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.8

The structure of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose also contains other interesting chemical elements:

Magnesium	(Mg)	9 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose (pdb code 6b5e). 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 Rmla in Complex with Dtdp-Glucose, PDB code: 6b5e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:32.9 occ:1.00 OD1 B:ASP100 2.2 19.6 1.0 O B:HOH568 2.3 33.4 1.0 O B:HOH648 2.3 39.3 1.0 O B:HOH582 2.4 36.4 1.0 O B:HOH517 2.7 22.3 1.0 CG B:ASP100 3.3 20.2 1.0 OD2 B:ASP100 3.9 20.1 1.0 N B:MET1 4.0 17.7 1.0 OG B:SER101 4.0 17.4 1.0 N B:SER101 4.3 14.6 1.0 O B:HOH476 4.3 30.7 1.0 CB B:ASP100 4.4 20.5 1.0 CA B:ASP100 4.5 18.0 1.0 O B:HOH628 4.6 41.4 1.0 CA B:MET1 4.7 16.2 1.0 O B:HOH483 4.8 25.3 1.0 O B:HOH608 4.8 37.8 1.0 O B:HOH653 4.9 32.9 1.0 CB B:SER101 4.9 13.9 1.0 O B:GLN124 4.9 20.4 1.0 C B:ASP100 5.0 16.9 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Tuberculosis Rmla in Complex with Dtdp-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:17.3 occ:1.00 O C:THR18 2.6 16.8 1.0 O C:HOH438 2.7 27.3 1.0 O C:HOH437 2.8 24.8 1.0 O C:HOH541 3.0 11.8 1.0 O C:ILE21 3.1 18.8 1.0 O C:HOH504 3.1 30.0 1.0 O C:SER10 3.1 24.5 1.0 O C:HOH548 3.7 32.4 1.0 C C:THR18 3.8 16.6 1.0 C C:ILE21 3.9 17.6 1.0 C C:SER10 4.0 23.8 1.0 CB C:THR18 4.0 14.5 1.0 CA C:SER22 4.1 16.5 1.0 N C:SER22 4.3 17.5 1.0 CA C:THR18 4.3 14.5 1.0 CA C:SER10 4.5 25.0 1.0 OD2 C:ASP57 4.5 18.6 1.0 O C:HOH423 4.6 23.0 1.0 O C:GLY9 4.6 19.8 1.0 CG2 C:THR18 4.7 15.2 1.0 N C:ILE21 4.7 17.5 1.0 O C:HOH473 4.8 25.1 1.0 OD1 C:ASP57 4.8 18.0 1.0 N C:GLY11 4.8 22.1 1.0 N C:MET19 4.9 16.0 1.0 N C:LYS23 4.9 15.4 1.0 CA C:ILE21 4.9 19.5 1.0 OG1 C:THR18 4.9 14.7 1.0 O C:MET19 5.0 26.6 1.0 C C:SER22 5.0 15.9 1.0

H.A.Brown, J.B.Thoden, P.A.Tipton, H.M.Holden. The Structure of Glucose-1-Phosphate Thymidylyltransferase From Mycobacterium Tuberculosis Reveals the Location of An Essential Magnesium Ion in the Rmla-Type Enzymes. Protein Sci. V. 27 441 2018.
ISSN: ESSN 1469-896X
PubMed: 29076563
DOI: 10.1002/PRO.3333