Sodium in PDB 6rlg: Crystal Structure of LDTMT2 From Mycobacterium Tuberculosis

The structure of Crystal Structure of LDTMT2 From Mycobacterium Tuberculosis, PDB code: 6rlg was solved by J.Brem, C.Lohans, C.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.950, 93.920, 75.570, 90.00, 93.03, 90.00
R / Rfree (%)	18 / 20.4

The binding sites of Sodium atom in the Crystal Structure of LDTMT2 From Mycobacterium Tuberculosis (pdb code 6rlg). 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 From Mycobacterium Tuberculosis, PDB code: 6rlg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of LDTMT2 From Mycobacterium Tuberculosis


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 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:45.9 occ:1.00 H A:ILE190 2.2 23.3 0.5 H A:ILE190 2.3 23.3 0.5 HA A:LYS189 2.8 26.3 1.0 HG12 A:ILE190 2.9 24.3 0.5 O A:ILE188 3.0 21.6 1.0 N A:ILE190 3.1 19.4 0.5 N A:ILE190 3.1 19.4 0.5 O A:HOH758 3.2 27.1 1.0 HB A:ILE190 3.3 22.9 0.5 HB A:ILE190 3.4 22.9 0.5 CA A:LYS189 3.6 21.9 1.0 HZ A:PHE200 3.7 25.1 1.0 HE2 A:PHE200 3.7 25.5 1.0 CG1 A:ILE190 3.7 20.2 0.5 C A:LYS189 3.9 19.3 1.0 CB A:ILE190 3.9 19.0 0.5 HG13 A:ILE190 3.9 23.2 0.5 C A:ILE188 4.0 20.1 1.0 CA A:ILE190 4.0 20.3 0.5 HD11 A:ILE190 4.0 22.5 0.5 CB A:ILE190 4.0 19.0 0.5 CA A:ILE190 4.1 20.1 0.5 HG13 A:ILE190 4.1 24.3 0.5 O A:HOH815 4.2 29.2 1.0 O A:ILE190 4.2 20.6 0.5 N A:LYS189 4.3 19.2 1.0 O A:ILE190 4.3 20.5 0.5 CE2 A:PHE200 4.3 21.2 1.0 CZ A:PHE200 4.3 20.9 1.0 CG1 A:ILE190 4.4 19.3 0.5 HE1 A:TRP210 4.4 23.2 1.0 HG22 A:ILE188 4.5 23.8 1.0 O A:HOH1014 4.5 54.6 1.0 C A:ILE190 4.6 19.4 0.5 C A:ILE190 4.7 19.5 0.5 CD1 A:ILE190 4.7 18.7 0.5 CB A:LYS189 4.8 26.4 1.0 HA A:ILE190 4.8 24.4 0.5 NE1 A:TRP210 4.8 19.3 1.0 HA A:ILE190 4.9 24.2 0.5 HD13 A:ILE190 4.9 22.9 0.5 CD1 A:ILE190 4.9 19.1 0.5 CG A:LYS189 5.0 31.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of LDTMT2 From Mycobacterium Tuberculosis


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 From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:42.4 occ:1.00 H A:ASP251 1.9 25.6 1.0 N A:ASP251 2.8 21.3 1.0 HA3 A:GLY250 2.8 25.0 1.0 HE3 A:LYS370 2.8 31.7 1.0 HB2 A:ASP251 3.0 34.1 1.0 HZ1 A:LYS370 3.3 31.4 1.0 CA A:GLY250 3.5 20.8 1.0 CB A:ASP251 3.5 28.4 1.0 OD2 A:ASP251 3.6 40.6 1.0 CG A:ASP251 3.6 36.6 1.0 C A:GLY250 3.6 21.0 1.0 CE A:LYS370 3.6 26.4 1.0 O A:HOH918 3.7 84.3 1.0 HZ3 A:LYS370 3.7 31.4 1.0 HA2 A:GLY250 3.7 25.0 1.0 NZ A:LYS370 3.7 26.2 1.0 CA A:ASP251 3.7 23.5 1.0 HG11 A:VAL163 3.9 25.1 1.0 HD3 A:LYS370 4.0 30.1 1.0 HG12 A:VAL163 4.1 25.1 1.0 OD1 A:ASP251 4.3 40.0 1.0 HE2 A:LYS370 4.3 31.7 1.0 HA A:ASP251 4.4 28.2 1.0 CG1 A:VAL163 4.4 20.9 1.0 CD A:LYS370 4.4 25.0 1.0 HB3 A:ASP251 4.4 34.1 1.0 O A:HOH938 4.5 46.4 1.0 HZ2 A:LYS370 4.6 31.4 1.0 HG13 A:VAL163 4.7 25.1 1.0 HD2 A:LYS370 4.7 30.1 1.0 O A:ASP251 4.7 22.9 1.0 C A:ASP251 4.8 22.4 1.0 N A:GLY250 4.8 20.9 1.0 O A:GLY250 4.8 21.7 1.0 H A:GLY250 4.8 25.2 1.0

M.De Munnik, C.T.Lohans, P.A.Lang, G.W.Langley, T.R.Malla, A.Tumber, C.J.Schofield, J.Brem. Targeting the Mycobacterium Tuberculosis Transpeptidase LDTMT2WITH Cysteine-Reactive Inhibitors Including Ebselen. Chem.Commun.(Camb.) V. 55 10214 2019.
ISSN: ESSN 1364-548X
PubMed: 31380528
DOI: 10.1039/C9CC04145A