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

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

The structure of Pseudomonas Aeruginosa Seryl-Trna Synthetase in Complex with 5'-O-(N- (L-Seryl)-Sulfamoyl)Uridine, PDB code: 6hdz 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)	91.47 / 2.06
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.559, 122.275, 65.473, 90.00, 114.56, 90.00
R / Rfree (%)	18.8 / 21.5

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


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)Uridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:66.5 occ:1.00 OE1 A:GLU351 2.3 42.6 1.0 O1S A:FZK504 2.5 38.8 1.0 OG A:SER354 2.5 53.1 1.0 O A:HOH787 2.6 65.7 1.0 CD A:GLU351 3.3 47.4 1.0 O A:HOH788 3.4 55.0 1.0 OE2 A:GLU351 3.6 46.4 1.0 O A:HOH790 3.7 57.4 1.0 CB A:SER354 3.7 38.2 1.0 S A:FZK504 3.8 37.5 1.0 O3' A:FZK504 4.1 35.9 1.0 OD2 A:ASP338 4.2 52.4 1.0 OD1 A:ASP338 4.3 44.8 1.0 C3' A:FZK504 4.3 38.0 1.0 O2S A:FZK504 4.4 35.2 1.0 CG A:GLU351 4.6 39.5 1.0 CG A:ASP338 4.6 46.3 1.0 O A:HOH687 4.6 60.8 1.0 O A:HOH676 4.7 42.2 1.0 O5' A:FZK504 4.7 36.3 1.0 N3S A:FZK504 4.7 39.2 1.0 CA A:SER354 4.9 33.9 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)Uridine


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)Uridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:62.7 occ:1.00 O1S B:FZK504 2.3 40.5 1.0 OE1 B:GLU351 2.4 45.6 1.0 O B:HOH706 2.4 46.6 1.0 O B:HOH707 3.3 62.3 1.0 O B:HOH745 3.4 47.3 1.0 CD B:GLU351 3.4 54.6 1.0 O B:HOH666 3.5 52.8 1.0 S B:FZK504 3.6 40.5 1.0 OE2 B:GLU351 3.8 55.3 1.0 OG B:SER354 3.8 49.5 1.0 CB B:SER354 3.9 39.4 1.0 O3' B:FZK504 4.0 39.7 1.0 O2S B:FZK504 4.2 38.8 1.0 C3' B:FZK504 4.3 40.1 1.0 OD2 B:ASP338 4.5 49.5 1.0 O5' B:FZK504 4.5 40.7 1.0 N3S B:FZK504 4.6 39.4 1.0 O B:HOH682 4.6 46.4 1.0 CG B:GLU351 4.7 44.8 1.0 OD1 B:ASP338 4.8 43.4 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.