Sodium in PDB 6vuy: Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358

The structure of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358, PDB code: 6vuy was solved by A.Punetha, C.Hou, H.X.Ngo, S.Garneau-Tsodikova, O.V.Tsodikov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 2.70
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	175.047, 175.047, 123.557, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 21.3

The structure of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 (pdb code 6vuy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358, PDB code: 6vuy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358


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 Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:64.9 occ:1.00 O A:GLY123 2.5 49.7 1.0 CH2 A:TRP295 3.3 32.8 1.0 C A:GLY123 3.7 50.9 1.0 CZ3 A:TRP295 4.0 32.4 1.0 CZ2 A:TRP295 4.2 31.3 1.0 CA A:GLY123 4.5 52.9 1.0 N A:GLY124 4.7 49.9 1.0 CG A:PRO133 4.8 30.6 1.0 CD A:PRO133 4.9 30.5 1.0 CA A:GLY124 4.9 51.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358


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 Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:51.5 occ:1.00 OG A:SER239 2.7 36.2 1.0 OG A:SER214 2.9 44.3 1.0 CB A:SER239 3.2 35.4 1.0 O A:HOH696 3.5 42.8 1.0 O A:HOH741 3.6 52.0 1.0 NH1 A:ARG227 3.6 53.9 1.0 CB A:SER214 3.8 41.9 1.0 C A:TYR226 4.0 34.2 1.0 N A:TYR226 4.0 33.8 1.0 C A:LEU225 4.0 34.2 1.0 CB A:LEU225 4.1 37.1 1.0 N A:ARG227 4.1 35.7 1.0 O A:LEU225 4.1 35.6 1.0 CA A:TYR226 4.1 33.5 1.0 O A:TYR226 4.2 34.0 1.0 CZ A:ARG227 4.2 55.5 1.0 N A:SER239 4.3 32.3 1.0 CB A:ARG227 4.3 39.3 1.0 CD A:ARG227 4.3 50.7 1.0 CA A:SER239 4.4 34.2 1.0 CG A:ARG227 4.4 45.5 1.0 NE A:ARG227 4.5 54.0 1.0 CA A:LEU225 4.7 34.1 1.0 O A:ARG237 4.7 29.9 1.0 CA A:SER214 4.8 39.9 1.0 CA A:ARG227 4.9 35.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:60.0 occ:1.00 O A:GLY315 2.9 51.7 1.0 NE A:ARG385 3.2 48.9 1.0 CZ A:ARG385 3.5 52.0 1.0 O A:GLU316 3.5 43.8 1.0 CD A:ARG385 3.5 47.3 1.0 C A:GLY315 3.6 50.2 1.0 NH2 A:ARG385 3.9 53.4 1.0 CB A:PHE317 3.9 42.7 1.0 N A:GLY315 3.9 47.2 1.0 CG A:ARG385 3.9 44.5 1.0 CA A:GLY315 4.0 49.1 1.0 NH1 A:ARG385 4.0 56.1 1.0 C A:GLU316 4.1 44.7 1.0 CG2 A:VAL314 4.2 48.2 1.0 CD1 A:PHE317 4.4 39.9 1.0 N A:GLU316 4.4 48.7 1.0 CG A:PHE317 4.5 40.6 1.0 N A:PHE317 4.6 42.5 1.0 O A:HOH636 4.7 43.2 1.0 CA A:PHE317 4.7 44.5 1.0 C A:VAL314 4.9 46.1 1.0 CA A:GLU316 4.9 48.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Eis From Mycobacterium Tuberculosis in Complex with Inhibitor SGT358 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:61.0 occ:1.00 OE1 A:GLU213 2.6 74.2 1.0 O A:SER214 2.9 36.1 1.0 CD A:GLU213 3.4 70.7 1.0 CG A:GLU213 3.5 65.5 1.0 CD1 A:PHE215 3.5 36.5 1.0 CE1 A:PHE215 3.6 36.2 1.0 CD A:PRO168 3.7 46.8 1.0 C A:SER214 3.9 36.4 1.0 CG A:ARG167 4.0 57.0 1.0 NH1 A:ARG167 4.0 67.1 1.0 CA A:ARG167 4.2 44.5 1.0 CG A:PHE215 4.4 36.0 1.0 CA A:PHE215 4.5 33.4 1.0 CB A:ARG167 4.5 50.9 1.0 CZ A:PHE215 4.5 36.7 1.0 N A:PHE215 4.5 34.5 1.0 CB A:GLU213 4.5 58.7 1.0 OE2 A:GLU213 4.6 68.5 1.0 N A:SER214 4.7 42.5 1.0 CG A:PRO168 4.7 46.7 1.0 N A:PRO168 4.8 45.3 1.0 O A:ALA204 4.9 70.2 1.0 CA A:SER214 4.9 39.9 1.0

A.Punetha, H.X.Ngo, S.Y.L.Holbrook, K.D.Green, M.J.Willby, S.A.Bonnett, K.Krieger, E.K.Dennis, J.E.Posey, T.Parish, O.V.Tsodikov, S.Garneau-Tsodikova. Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis Frommycobacterium Tuberculosis. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 32421305
DOI: 10.1021/ACSCHEMBIO.0C00184