Sodium in PDB 5c80: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution:
2.4.2.3;

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution, PDB code: 5c80 was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.47 / 2.24
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.255, 73.110, 83.137, 71.81, 77.19, 85.69
R / Rfree (%)	16.8 / 23.7

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution (pdb code 5c80). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution, PDB code: 5c80:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:26.5 occ:1.00 OE2 A:GLU48 2.7 34.1 1.0 O B:ILE68 2.8 20.2 1.0 OE2 B:GLU48 2.8 28.7 1.0 OG A:SER72 2.8 24.5 1.0 OG B:SER72 2.9 21.4 1.0 O A:ILE68 3.0 20.5 1.0 N B:ILE68 3.4 20.7 1.0 CB B:SER72 3.5 20.0 1.0 CB A:SER72 3.5 22.9 1.0 O B:HOH436 3.6 27.7 1.0 C B:ILE68 3.7 21.0 1.0 CD A:GLU48 3.8 33.3 1.0 N A:ILE68 3.9 22.7 1.0 CD B:GLU48 3.9 28.1 1.0 C B:GLY67 4.0 20.4 1.0 CA B:ILE68 4.1 20.3 1.0 C A:ILE68 4.1 20.4 1.0 CA B:GLY67 4.1 20.9 1.0 CG B:GLU48 4.3 26.2 1.0 CG A:GLU48 4.4 31.1 1.0 C A:GLY67 4.4 23.5 1.0 CA A:GLY67 4.5 23.5 1.0 CA A:ILE68 4.5 21.3 1.0 CB B:ILE68 4.6 20.1 1.0 O B:THR66 4.6 24.3 1.0 CA B:SER72 4.8 21.4 1.0 CA A:SER72 4.9 23.5 1.0 OE1 A:GLU48 4.9 32.4 1.0 N B:GLY69 4.9 21.6 1.0 CB A:ILE68 4.9 21.5 1.0 O A:THR66 4.9 26.3 1.0 O B:GLY67 5.0 21.0 1.0 OE1 B:GLU48 5.0 30.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 2.24 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Na307 b:36.3 occ:1.00 OE2 F:GLU48 2.7 22.3 1.0 OE2 E:GLU48 2.8 30.4 1.0 O F:ILE68 3.0 17.2 1.0 O E:ILE68 3.0 21.3 1.0 OG F:SER72 3.1 20.0 1.0 OG E:SER72 3.2 19.1 1.0 CB F:SER72 3.4 20.4 1.0 CB E:SER72 3.5 19.4 1.0 N F:ILE68 3.5 18.5 1.0 N E:ILE68 3.6 23.1 1.0 O F:HOH431 3.7 43.5 1.0 CD F:GLU48 3.8 22.4 1.0 CD E:GLU48 3.9 28.9 1.0 C F:ILE68 3.9 17.6 1.0 C E:ILE68 4.0 21.4 1.0 C F:GLY67 4.2 18.5 1.0 CA F:ILE68 4.2 17.8 1.0 C E:GLY67 4.2 24.3 1.0 CA E:GLY67 4.2 25.1 1.0 CA F:GLY67 4.2 18.4 1.0 CG E:GLU48 4.3 27.8 1.0 CA E:ILE68 4.3 22.2 1.0 CG F:GLU48 4.4 22.8 1.0 CB F:ILE68 4.7 17.6 1.0 CB E:ILE68 4.7 22.3 1.0 CA F:SER72 4.7 20.1 1.0 O E:THR66 4.8 26.1 1.0 O F:THR66 4.8 20.2 1.0 OE1 F:GLU48 4.8 22.8 1.0 CA E:SER72 4.9 20.6 1.0 OE1 E:GLU48 4.9 27.1 1.0 CB F:GLU48 5.0 23.7 1.0 CB E:GLU48 5.0 28.6 1.0 N F:SER72 5.0 19.4 1.0

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, V.V.Balaev, T.A.Seregina, A.S.Mironov, C.Betzel, A.M.Mikhailov. X-Ray Structures of Uridine Phosphorylase From Vibrio Cholerae in Complexes with Uridine, Thymidine, Uracil, Thymine, and Phosphate Anion: Substrate Specificity of Bacterial Uridine Phosphorylases Crystallography Reports V. 61 954 2016.
ISSN: ISSN 1063-7745
DOI: 10.1134/S1063774516060134