Sodium in PDB 6he1: Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine

All present enzymatic activity of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine:
6.1.1.11;

The structure of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine, PDB code: 6he1 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)	32.50 / 2.22
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.948, 121.841, 65.281, 90.00, 113.83, 90.00
R / Rfree (%)	18.7 / 21.4

The binding sites of Sodium atom in the Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)N3-Methyluridine (pdb code 6he1). 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)N3-Methyluridine, PDB code: 6he1:
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)N3-Methyluridine


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)N3-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:77.3 occ:1.00 OG A:SER354 2.4 56.7 1.0 OE2 A:GLU351 2.5 56.3 1.0 O A:HOH696 2.5 75.3 1.0 O2S A:FZT504 2.8 51.7 1.0 CD A:GLU351 3.3 56.7 1.0 CB A:SER354 3.5 45.3 1.0 OE1 A:GLU351 3.6 68.8 1.0 OD2 A:ASP338 4.0 66.2 1.0 OD1 A:ASP338 4.1 58.2 1.0 S A:FZT504 4.1 50.4 1.0 O A:HOH697 4.2 58.2 1.0 O3' A:FZT504 4.3 48.1 1.0 CG A:ASP338 4.4 57.5 1.0 CG A:GLU351 4.6 48.7 1.0 O A:HOH654 4.6 56.9 1.0 C3' A:FZT504 4.6 45.9 1.0 CA A:SER354 4.7 42.7 1.0 O1S A:FZT504 4.8 50.5 1.0 N3S A:FZT504 4.9 47.1 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)N3-Methyluridine


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)N3-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:77.1 occ:1.00 O B:HOH651 2.2 58.4 1.0 OE1 B:GLU351 2.4 49.1 1.0 O2S B:FZT504 2.5 49.6 1.0 OG B:SER354 3.1 64.7 1.0 CD B:GLU351 3.5 66.5 1.0 CB B:SER354 3.6 50.0 1.0 S B:FZT504 3.9 53.2 1.0 OE2 B:GLU351 4.0 64.2 1.0 O3' B:FZT504 4.1 53.1 1.0 O B:HOH670 4.1 56.5 1.0 OD2 B:ASP338 4.1 60.2 1.0 OD1 B:ASP338 4.2 60.0 1.0 C3' B:FZT504 4.5 50.7 1.0 O B:HOH656 4.5 50.4 1.0 O1S B:FZT504 4.5 54.1 1.0 CG B:ASP338 4.6 58.4 1.0 N3S B:FZT504 4.6 52.4 1.0 CG B:GLU351 4.7 48.8 1.0 CA B:SER354 4.8 45.7 1.0 O5' B:FZT504 4.9 49.7 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.