Sodium in PDB 4huc: Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C

The structure of Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C, PDB code: 4huc was solved by D.Both, E.Steiner, Y.Lindqvist, R.Schnell, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.00 / 1.86
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.027, 121.430, 123.298, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.8

The binding sites of Sodium atom in the Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C (pdb code 4huc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C, PDB code: 4huc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:27.4 occ:1.00 O A:HOH774 2.2 27.2 1.0 O A:VAL342 2.3 19.1 1.0 O A:HOH653 2.4 36.1 1.0 O A:GLN345 2.5 16.2 1.0 O A:HOH713 2.5 24.5 0.7 O A:GLY343 2.8 18.6 1.0 C A:GLY343 3.3 17.9 1.0 C A:VAL342 3.5 17.1 1.0 C A:GLN345 3.5 16.0 1.0 CA A:GLY343 3.6 17.7 1.0 N A:GLN345 3.8 15.0 1.0 CD2 A:HIS347 3.9 27.3 1.0 CA A:GLN345 4.0 15.3 1.0 N A:GLY343 4.0 17.2 1.0 CB A:GLN345 4.1 15.4 1.0 N A:ALA344 4.2 15.4 1.0 C A:ALA344 4.3 16.4 1.0 NE2 A:HIS347 4.3 30.2 1.0 O A:HOH776 4.4 34.8 1.0 O A:HOH636 4.6 25.5 1.0 CA A:VAL342 4.7 16.1 1.0 N A:GLY346 4.7 15.6 1.0 CA A:ALA344 4.8 16.0 1.0 O A:ALA344 4.8 17.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of LDTMT2, A L,D-Transpeptidase From Mycobacterium Tuberculosis: Domain B and C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:29.1 occ:1.00 O B:VAL342 2.3 16.4 1.0 O B:HOH754 2.4 28.5 1.0 O B:GLN345 2.5 18.2 1.0 O B:HOH633 2.7 38.4 1.0 O B:GLY343 2.8 18.6 1.0 C B:GLY343 3.4 18.4 1.0 C B:VAL342 3.5 17.0 1.0 C B:GLN345 3.6 17.9 1.0 CA B:GLY343 3.8 17.6 1.0 CD2 B:HIS347 3.8 32.1 1.0 N B:GLN345 3.8 15.6 1.0 CA B:GLN345 4.1 16.3 1.0 N B:GLY343 4.1 16.1 1.0 NE2 B:HIS347 4.2 34.7 1.0 N B:ALA344 4.2 16.5 1.0 CB B:GLN345 4.2 16.0 1.0 O A:HOH799 4.3 37.0 1.0 C B:ALA344 4.3 16.2 1.0 CA B:VAL342 4.7 15.8 1.0 O B:HOH638 4.7 24.7 1.0 CA B:ALA344 4.8 16.8 1.0 N B:GLY346 4.8 16.5 1.0 O B:ALA344 4.9 17.1 1.0

D.Both, E.M.Steiner, D.Stadler, Y.Lindqvist, R.Schnell, G.Schneider. Structure of LDTMT2, An L,D-Transpeptidase From Mycobacterium Tuberculosis. Acta Crystallogr.,Sect.D V. 69 432 2013.
ISSN: ISSN 0907-4449
PubMed: 23519418
DOI: 10.1107/S0907444912049268