Sodium in PDB 8aho: Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31

The structure of Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31, PDB code: 8aho was solved by M.De Munnik, P.A.Lang, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.18 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.25, 94.261, 75.667, 90, 92.69, 90
R / Rfree (%)	20.9 / 24.8

The structure of Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31 (pdb code 8aho). 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 the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31, PDB code: 8aho:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31


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 the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:53.5 occ:1.00 O A:ASN121 3.4 55.7 1.0 C A:ARG122 3.6 44.5 1.0 N A:ARG123 3.6 40.9 1.0 CB A:ARG123 3.9 41.1 1.0 OD2 A:ASP96 3.9 52.8 1.0 CA A:ARG122 3.9 42.1 1.0 C A:ASN121 3.9 47.8 1.0 O A:ARG122 4.0 41.9 1.0 N A:ARG122 4.2 41.6 1.0 CA A:ARG123 4.3 39.1 1.0 CG A:GLN144 4.4 62.0 1.0 OD1 A:ASN121 4.6 67.5 1.0 CD A:GLN144 4.6 69.3 1.0 CG A:ASP96 4.8 66.2 1.0 NE2 A:GLN144 4.9 64.6 1.0 CG A:ASN121 4.9 57.4 1.0 CA A:ASN121 4.9 50.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31


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 the Transpeptidase LDTMT2 From Mycobacterium Tuberculosis in Complex with Cyanamide Analogue 31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:43.2 occ:1.00 OH B:TYR124 3.2 37.5 1.0 O B:HOH852 3.4 46.6 1.0 O B:HOH760 3.6 49.8 1.0 ND2 B:ASN95 3.9 55.8 1.0 NH2 B:ARG122 4.1 65.7 1.0 CZ B:TYR124 4.2 41.0 1.0 CE1 B:TYR124 4.2 34.3 1.0 CG2 B:VAL101 4.5 41.2 1.0 CZ B:ARG122 4.6 68.3 1.0 NE B:ARG122 4.6 66.5 1.0 CB B:ASN95 4.7 47.2 1.0 CG B:ASN95 4.8 48.7 1.0 N B:GLY119 4.9 36.4 1.0 O B:GLN117 4.9 43.7 1.0 O B:HOH734 5.0 38.3 1.0

M.De Munnik, P.A.Lang, F.De Dios Anton, M.Cacho, R.H.Bates, J.Brem, B.Rodriguez Miquel, C.J.Schofield. High-Throughput Screen with the L,D-Transpeptidase Ldt MT2 of Mycobacterium Tuberculosis Reveals Novel Classes of Covalently Reacting Inhibitors. Chem Sci V. 14 7262 2023.
ISSN: ISSN 2041-6520
PubMed: 37416715
DOI: 10.1039/D2SC06858C