Sodium in PDB 4oeh: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution

All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution:
2.4.2.3;

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution, PDB code: 4oeh 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)	44.28 / 1.91
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.255, 71.763, 89.321, 69.14, 72.15, 85.79
R / Rfree (%)	17.2 / 21.6

The binding sites of Sodium atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution (pdb code 4oeh). 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 of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution, PDB code: 4oeh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 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 of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:35.3 occ:0.93 OE2 B:GLU48 2.3 24.5 1.0 OE2 A:GLU48 2.4 23.4 1.0 OG A:SER72 3.0 16.8 0.5 O A:ILE68 3.1 18.2 1.0 OG B:SER72 3.2 16.6 0.4 O B:ILE68 3.2 17.1 1.0 OG B:SER72 3.2 17.0 0.6 CB B:SER72 3.3 17.0 0.6 CB A:SER72 3.4 17.3 0.5 CB A:SER72 3.4 17.3 0.5 N A:ILE68 3.4 18.6 1.0 CB B:SER72 3.4 17.2 0.4 CD B:GLU48 3.5 26.4 1.0 N B:ILE68 3.5 18.8 1.0 OG A:SER72 3.5 17.6 0.5 CD A:GLU48 3.5 25.1 1.0 O A:HOH421 3.9 19.4 1.0 C A:ILE68 4.0 18.0 1.0 C B:ILE68 4.1 17.3 1.0 CG A:GLU48 4.1 24.4 1.0 C A:GLY67 4.1 18.5 1.0 CA B:GLY67 4.1 20.0 1.0 CA A:GLY67 4.1 18.6 1.0 CA A:ILE68 4.2 18.3 1.0 CG B:GLU48 4.2 25.0 1.0 C B:GLY67 4.2 19.4 1.0 CA B:ILE68 4.2 17.9 1.0 OE1 B:GLU48 4.4 26.0 1.0 OE1 A:GLU48 4.5 24.3 1.0 CB A:ILE68 4.6 18.3 1.0 CB B:ILE68 4.6 18.0 1.0 CA B:SER72 4.7 16.7 0.6 O A:THR66 4.7 18.5 1.0 CA A:SER72 4.8 16.9 0.5 O B:THR66 4.8 20.7 1.0 CB B:GLU48 4.8 24.5 1.0 CA A:SER72 4.9 16.9 0.5 CA B:SER72 4.9 16.7 0.4 CB A:GLU48 4.9 24.3 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 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 of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na303 b:31.6 occ:0.86 OE2 C:GLU48 2.4 27.3 1.0 OE2 D:GLU48 2.4 25.8 1.0 O D:ILE68 3.0 19.8 1.0 OG D:SER72 3.0 16.6 0.5 O C:ILE68 3.1 19.5 1.0 OG C:SER72 3.3 16.2 0.4 CB D:SER72 3.3 17.2 0.5 CB D:SER72 3.4 17.1 0.5 N D:ILE68 3.4 20.4 1.0 CB C:SER72 3.4 16.8 0.6 OG D:SER72 3.4 17.3 0.5 CB C:SER72 3.4 16.7 0.4 CD D:GLU48 3.5 26.5 1.0 CD C:GLU48 3.5 27.6 1.0 OG C:SER72 3.6 17.2 0.6 N C:ILE68 3.6 19.8 1.0 C D:ILE68 3.9 19.9 1.0 O C:HOH446 3.9 18.9 1.0 C D:GLY67 4.0 20.7 1.0 CG D:GLU48 4.1 25.8 1.0 C C:ILE68 4.1 19.3 1.0 CA D:GLY67 4.1 21.3 1.0 CA D:ILE68 4.1 20.2 1.0 CG C:GLU48 4.2 26.8 1.0 CA C:GLY67 4.3 20.5 1.0 C C:GLY67 4.3 20.2 1.0 CA C:ILE68 4.3 19.8 1.0 CB D:ILE68 4.5 20.6 1.0 OE1 C:GLU48 4.5 27.8 1.0 OE1 D:GLU48 4.5 26.2 1.0 CB C:ILE68 4.7 20.5 1.0 O D:THR66 4.7 21.0 1.0 CA D:SER72 4.7 17.0 0.5 CA D:SER72 4.8 16.9 0.5 CA C:SER72 4.8 16.5 0.6 CA C:SER72 4.8 16.4 0.4 CB D:GLU48 4.9 25.9 1.0 CB C:GLU48 5.0 26.0 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 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 of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Na305 b:21.0 occ:0.74 OE2 E:GLU48 2.4 23.3 1.0 OE2 F:GLU48 2.6 22.6 1.0 O F:ILE68 2.9 16.5 1.0 OG E:SER72 2.9 14.1 0.6 OG F:SER72 2.9 14.2 0.5 O E:ILE68 3.1 15.8 1.0 CB F:SER72 3.3 14.8 0.5 CB E:SER72 3.3 14.6 0.4 CB E:SER72 3.3 14.6 0.6 CB F:SER72 3.4 14.8 0.5 N F:ILE68 3.4 17.4 1.0 OG F:SER72 3.4 15.1 0.5 OG E:SER72 3.5 14.6 0.4 N E:ILE68 3.5 16.9 1.0 CD E:GLU48 3.5 24.6 1.0 O F:HOH460 3.6 20.2 1.0 CD F:GLU48 3.7 23.7 1.0 C F:ILE68 3.8 16.6 1.0 C E:ILE68 4.0 16.3 1.0 CA F:ILE68 4.0 16.9 1.0 C F:GLY67 4.1 17.6 1.0 CA F:GLY67 4.1 18.0 1.0 C E:GLY67 4.2 17.8 1.0 CG E:GLU48 4.2 23.4 1.0 CA E:GLY67 4.2 18.2 1.0 CA E:ILE68 4.3 16.4 1.0 CG F:GLU48 4.3 22.6 1.0 CB F:ILE68 4.5 17.4 1.0 OE1 E:GLU48 4.5 24.6 1.0 CA F:SER72 4.7 14.5 0.5 OE1 F:GLU48 4.7 23.7 1.0 CA E:SER72 4.7 14.4 0.4 CA F:SER72 4.7 14.4 0.5 CA E:SER72 4.7 14.3 0.6 O E:THR66 4.8 18.7 1.0 CB E:ILE68 4.8 16.7 1.0 O F:THR66 4.8 17.8 1.0 CB E:GLU48 4.9 24.0 1.0 N F:SER72 5.0 14.2 1.0

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae Complexed with Uracil at 1.91 A Resolution To Be Published.