Sodium in PDB 5vev: Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae

All present enzymatic activity of Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae:
6.3.4.13;

The structure of Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae, PDB code: 5vev was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.52 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.310, 99.450, 131.600, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.1

The binding sites of Sodium atom in the Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae (pdb code 5vev). 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 Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae, PDB code: 5vev:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae


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 Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:27.1 occ:1.00 O A:ARG288 2.3 27.2 1.0 OD2 A:ASP212 2.3 25.1 1.0 O A:GLY226 2.4 26.2 1.0 O A:ASP291 2.4 25.3 1.0 OE1 A:GLU293 2.5 22.9 1.0 OE2 A:GLU293 3.1 22.2 1.0 CD A:GLU293 3.2 28.4 1.0 C A:ASP291 3.2 21.1 1.0 NZ A:LYS214 3.3 33.6 1.0 CG A:ASP212 3.3 27.6 1.0 C A:ARG288 3.4 27.6 1.0 CD A:PRO292 3.4 25.3 1.0 C A:GLY226 3.6 31.9 1.0 N A:PRO292 3.7 24.1 1.0 CE A:LYS214 3.9 35.6 1.0 CA A:GLY227 3.9 28.0 1.0 O A:HOH766 4.0 31.3 1.0 N A:ASP291 4.0 23.3 1.0 OD1 A:ASP212 4.1 27.2 1.0 CA A:ARG288 4.2 31.8 1.0 CB A:ASP212 4.2 21.8 1.0 N A:GLY227 4.2 29.6 1.0 CA A:PHE289 4.2 23.4 1.0 N A:PHE289 4.2 23.5 1.0 CA A:ASP291 4.3 19.3 1.0 NH1 A:ARG380 4.5 25.8 1.0 N A:GLY290 4.6 23.1 1.0 C A:PHE289 4.6 23.0 1.0 CG A:GLU293 4.6 20.6 1.0 CB A:ARG288 4.7 35.5 1.0 CG A:LYS214 4.8 33.1 1.0 CA A:GLY226 4.8 27.1 1.0 N A:GLU293 4.8 16.9 1.0 CG A:PRO292 4.8 25.5 1.0 CD A:LYS214 5.0 38.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae


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 Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:36.7 occ:1.00 O B:ARG288 2.2 42.0 1.0 OD2 B:ASP212 2.2 39.1 1.0 O B:ASP291 2.4 38.0 1.0 OE1 B:GLU293 2.5 35.9 1.0 O B:GLY226 2.5 41.0 1.0 OE2 B:GLU293 3.1 37.1 1.0 CD B:GLU293 3.1 41.6 1.0 C B:ASP291 3.2 35.7 1.0 CG B:ASP212 3.3 43.4 1.0 C B:ARG288 3.3 39.4 1.0 CD B:PRO292 3.4 45.0 1.0 NZ B:LYS214 3.5 43.3 1.0 N B:PRO292 3.6 36.1 1.0 C B:GLY226 3.7 44.6 1.0 N B:ASP291 4.0 30.6 1.0 OD1 B:ASP212 4.0 41.0 1.0 CA B:GLY227 4.0 42.0 1.0 CE B:LYS214 4.1 53.0 1.0 N B:PHE289 4.1 38.5 1.0 CA B:PHE289 4.2 34.0 1.0 CB B:ASP212 4.2 42.3 1.0 CA B:ARG288 4.2 42.2 1.0 CA B:ASP291 4.2 31.2 1.0 N B:GLY227 4.3 42.5 1.0 NH1 B:ARG380 4.5 43.0 1.0 N B:GLY290 4.5 28.6 1.0 CG B:GLU293 4.5 34.2 1.0 C B:PHE289 4.5 32.1 1.0 N B:GLU293 4.8 32.5 1.0 CB B:ARG288 4.8 51.2 1.0 CA B:GLY226 4.8 43.9 1.0 CG B:PRO292 4.9 40.5 1.0 CG B:LYS214 4.9 50.0 1.0 CA B:PRO292 5.0 33.2 1.0

D.M.Dranow, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of Phosphoribosylamine-Glycine Ligase From Neisseria Gonorrhoeae To Be Published.