Sodium in PDB 6he3: Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine

All present enzymatic activity of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine:
6.1.1.11;

The structure of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine, PDB code: 6he3 was solved by L.Pang, S.De Graef, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.20 / 2.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.006, 122.183, 65.489, 90.00, 114.67, 90.00
R / Rfree (%)	18.7 / 21.5

The binding sites of Sodium atom in the Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine (pdb code 6he3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine, PDB code: 6he3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:56.0 occ:1.00 O A:HOH769 2.2 66.9 1.0 O2S A:FZQ504 2.4 39.2 1.0 OE1 A:GLU351 2.4 47.0 1.0 OG A:SER354 2.5 48.0 1.0 O A:HOH660 2.5 60.8 1.0 O A:HOH757 3.1 59.1 1.0 CD A:GLU351 3.4 46.4 1.0 CB A:SER354 3.6 38.3 1.0 O A:HOH772 3.7 57.6 1.0 OE2 A:GLU351 3.7 49.9 1.0 S A:FZQ504 3.7 40.2 1.0 O3' A:FZQ504 4.1 36.8 1.0 OD2 A:ASP338 4.2 55.5 1.0 OD1 A:ASP338 4.3 48.2 1.0 O1S A:FZQ504 4.4 37.7 1.0 C3' A:FZQ504 4.4 39.0 1.0 O A:HOH687 4.5 44.7 1.0 N3S A:FZQ504 4.6 38.5 1.0 CG A:GLU351 4.6 41.1 1.0 CG A:ASP338 4.6 50.0 1.0 O5' A:FZQ504 4.7 41.1 1.0 CA A:SER354 4.8 35.3 1.0

Sodium binding site 2 out of 2 in the Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Cytidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:63.3 occ:1.00 OE1 B:GLU351 2.3 44.9 1.0 O2S B:FZQ504 2.3 41.9 1.0 O B:HOH677 2.5 46.2 1.0 CD B:GLU351 3.4 62.1 1.0 O B:HOH631 3.4 58.7 1.0 OG B:SER354 3.5 53.5 1.0 O B:HOH731 3.6 56.4 1.0 O B:HOH717 3.6 75.0 1.0 S B:FZQ504 3.6 42.8 1.0 CB B:SER354 3.8 42.1 1.0 O3' B:FZQ504 3.9 41.3 1.0 OE2 B:GLU351 3.9 67.2 1.0 O1S B:FZQ504 4.2 41.8 1.0 O B:HOH694 4.2 72.7 1.0 C3' B:FZQ504 4.2 40.3 1.0 OD2 B:ASP338 4.3 47.7 1.0 N3S B:FZQ504 4.5 40.9 1.0 O5' B:FZQ504 4.6 42.2 1.0 O B:HOH668 4.6 52.2 1.0 OD1 B:ASP338 4.6 43.7 1.0 CG B:GLU351 4.6 50.4 1.0 CG B:ASP338 4.8 44.2 1.0

L.Pang, M.Nautiyal, S.De Graef, S.V.Strelkov, A.Van Aerschot, S.D.Weeks. Structural Insights Into the Binding of Natural Pyrimidine Based Inhibitors of Class II Aminoacyl-Trna Synthetase To Be Published.