Sodium in PDB 4ogl: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution:
2.4.2.3;

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution, PDB code: 4ogl 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)	8.00 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.748, 96.499, 92.776, 90.00, 119.99, 90.00
R / Rfree (%)	11.5 / 14.7

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution (pdb code 4ogl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution, PDB code: 4ogl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 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 Thymine at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:15.0 occ:0.49 OE1 B:GLU48 2.6 17.7 1.0 OE2 A:GLU48 2.6 13.4 0.7 OG A:SER72 2.9 8.8 0.5 O B:ILE68 2.9 10.7 1.0 OG B:SER72 2.9 9.3 0.5 O A:ILE68 2.9 11.4 1.0 CB A:SER72 3.2 10.8 0.5 CB B:SER72 3.2 9.4 0.5 OG A:SER72 3.2 10.9 0.5 OG B:SER72 3.3 9.1 0.5 CB A:SER72 3.3 9.8 0.5 CB B:SER72 3.3 9.7 0.5 N A:ILE68 3.5 10.6 1.0 N B:ILE68 3.5 10.1 1.0 O A:HOH458 3.6 10.5 0.5 O A:HOH458 3.7 13.4 0.5 CD B:GLU48 3.7 21.2 1.0 CD A:GLU48 3.8 15.9 0.7 C A:ILE68 3.8 9.0 1.0 C B:ILE68 3.8 8.7 1.0 CA A:ILE68 4.1 9.7 1.0 C A:GLY67 4.1 11.0 1.0 CA A:GLY67 4.1 11.1 1.0 CA B:ILE68 4.2 9.2 1.0 C B:GLY67 4.2 10.1 1.0 CA B:GLY67 4.2 10.2 1.0 CG A:GLU48 4.3 24.2 0.3 CG B:GLU48 4.4 21.7 1.0 CG A:GLU48 4.4 18.5 0.7 CD A:GLU48 4.5 27.9 0.3 CA A:SER72 4.5 9.4 0.5 CA B:SER72 4.5 8.7 0.5 CB A:ILE68 4.5 10.9 1.0 CB B:ILE68 4.6 10.6 1.0 CA A:SER72 4.6 9.1 0.5 CA B:SER72 4.7 8.6 0.5 OE2 B:GLU48 4.7 21.8 1.0 OE1 A:GLU48 4.8 30.7 0.3 OE1 A:GLU48 4.8 17.7 0.7 O A:THR66 4.9 12.0 1.0 N A:SER72 4.9 8.4 1.0 N B:SER72 4.9 8.1 1.0 OE2 A:GLU48 4.9 27.7 0.3 O B:THR66 4.9 11.3 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 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 Thymine at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:14.2 occ:0.50 OE2 D:GLU48 2.5 11.1 0.7 OE2 C:GLU48 2.5 11.0 0.7 OG D:SER72 2.9 8.7 0.5 O D:ILE68 2.9 10.1 1.0 OG C:SER72 2.9 9.0 0.5 O C:ILE68 2.9 9.6 1.0 CB C:SER72 3.1 9.3 0.5 CB D:SER72 3.2 9.1 0.5 OG C:SER72 3.2 9.2 0.5 OG D:SER72 3.2 9.1 0.5 CB C:SER72 3.3 9.6 0.5 CB D:SER72 3.3 9.4 0.5 N C:ILE68 3.4 9.7 1.0 N D:ILE68 3.5 9.4 1.0 O D:HOH466 3.6 12.8 0.5 O D:HOH466 3.7 10.0 0.5 CD D:GLU48 3.7 16.5 0.7 CD C:GLU48 3.7 16.0 0.7 C D:ILE68 3.8 8.8 1.0 C C:ILE68 3.8 8.3 1.0 CA C:ILE68 4.1 9.4 1.0 CA D:ILE68 4.1 9.5 1.0 C C:GLY67 4.1 9.7 1.0 C D:GLY67 4.2 9.6 1.0 CA C:GLY67 4.2 10.8 1.0 CA D:GLY67 4.2 9.8 1.0 CG C:GLU48 4.3 22.5 0.3 CG D:GLU48 4.4 18.8 0.7 CG C:GLU48 4.4 16.3 0.7 CA C:SER72 4.5 8.7 0.5 CB D:ILE68 4.5 10.3 1.0 CA D:SER72 4.5 8.2 0.5 CB C:ILE68 4.5 10.6 1.0 CD D:GLU48 4.6 23.6 0.3 CA C:SER72 4.6 8.7 0.5 CA D:SER72 4.6 8.2 0.5 OE1 D:GLU48 4.7 18.0 0.7 OE1 C:GLU48 4.7 20.5 0.7 OE1 D:GLU48 4.7 31.9 0.3 CG D:GLU48 4.8 21.9 0.3 CD C:GLU48 4.8 24.1 0.3 OE2 D:GLU48 4.9 20.0 0.3 OE1 C:GLU48 4.9 24.4 0.3 N C:SER72 4.9 8.0 1.0 N D:SER72 4.9 7.6 1.0 O C:THR66 4.9 10.7 1.0 O D:THR66 4.9 10.9 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Na305 b:14.8 occ:0.50 OE2 F:GLU48 2.6 19.8 1.0 OE2 E:GLU48 2.6 17.2 1.0 O E:ILE68 2.8 11.2 1.0 OG F:SER72 2.9 9.0 0.5 O F:ILE68 2.9 11.0 1.0 OG E:SER72 2.9 8.9 0.5 CB F:SER72 3.2 11.0 0.5 CB E:SER72 3.2 9.1 0.5 OG F:SER72 3.2 10.8 0.5 CB E:SER72 3.3 8.9 0.5 CB F:SER72 3.3 10.3 0.5 OG E:SER72 3.3 8.8 0.5 N E:ILE68 3.5 10.8 1.0 N F:ILE68 3.5 10.4 1.0 O E:HOH471 3.6 12.6 0.5 O E:HOH471 3.6 12.3 0.5 CD F:GLU48 3.8 22.5 1.0 CD E:GLU48 3.8 20.7 1.0 C E:ILE68 3.8 9.6 1.0 C F:ILE68 3.8 10.0 1.0 CA E:ILE68 4.1 10.3 1.0 CA F:ILE68 4.1 10.1 1.0 C F:GLY67 4.2 11.4 1.0 C E:GLY67 4.2 10.6 1.0 CA F:GLY67 4.2 11.5 1.0 CA E:GLY67 4.2 11.0 1.0 CG F:GLU48 4.4 22.8 1.0 CG E:GLU48 4.4 21.2 1.0 CA F:SER72 4.5 9.6 0.5 CB E:ILE68 4.5 11.6 1.0 CA E:SER72 4.5 8.4 0.5 CB F:ILE68 4.6 10.2 1.0 CA E:SER72 4.6 8.2 0.5 CA F:SER72 4.7 9.2 0.5 OE1 F:GLU48 4.7 23.9 1.0 OE1 E:GLU48 4.8 22.1 1.0 O F:THR66 4.9 13.4 1.0 N F:SER72 4.9 9.0 1.0 N E:SER72 4.9 7.9 1.0 O E:THR66 4.9 11.2 1.0 N E:GLY69 5.0 9.9 1.0

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymine at 1.25 A Resolution To Be Published.