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Sodium in PDB 5our: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A., PDB code: 5our was solved by I.I.Prokofev, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.A.Lashkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.60 / 1.35
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 93.245, 93.245, 152.928, 90.00, 90.00, 120.00
R / Rfree (%) 13.1 / 17.1

Other elements in 5our:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. (pdb code 5our). 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 2,2'-Anhydrouridine at 1.34 A., PDB code: 5our:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5our

Go back to Sodium Binding Sites List in 5our
Sodium binding site 1 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.


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 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:18.4
occ:1.00
OE2 A:GLU48 2.7 11.8 1.0
OE2 B:GLU48 2.8 12.1 1.0
OG B:SER72 3.0 7.8 1.0
OG A:SER72 3.0 8.1 1.0
O A:ILE68 3.0 8.6 1.0
O B:ILE68 3.0 8.2 1.0
CB B:SER72 3.4 8.9 1.0
CB A:SER72 3.4 8.0 1.0
N B:ILE68 3.6 7.5 1.0
O A:HOH497 3.6 7.1 0.5
O A:HOH497 3.6 7.0 0.5
N A:ILE68 3.6 7.5 1.0
CD A:GLU48 3.8 11.7 1.0
CD B:GLU48 3.8 12.5 1.0
C B:ILE68 3.9 7.3 1.0
C A:ILE68 3.9 8.0 1.0
CA B:GLY67 4.1 8.5 1.0
C B:GLY67 4.1 7.6 1.0
CA A:GLY67 4.1 8.4 1.0
C A:GLY67 4.2 7.9 1.0
CA B:ILE68 4.3 7.1 1.0
CA A:ILE68 4.3 7.2 1.0
CG B:GLU48 4.4 12.9 1.0
CG A:GLU48 4.4 12.0 1.0
CB B:ILE68 4.7 8.0 1.0
CB A:ILE68 4.7 8.1 1.0
CA B:SER72 4.8 7.4 1.0
CA A:SER72 4.8 6.8 1.0
OE1 B:GLU48 4.8 13.6 1.0
O B:THR66 4.8 10.3 1.0
OE1 A:GLU48 4.8 13.0 1.0
O A:THR66 4.8 9.6 1.0
N A:SER72 5.0 6.4 1.0
N B:SER72 5.0 6.2 1.0

Sodium binding site 2 out of 3 in 5our

Go back to Sodium Binding Sites List in 5our
Sodium binding site 2 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.


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 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:18.6
occ:1.00
OE2 D:GLU48 2.7 12.9 1.0
OE2 C:GLU48 2.7 13.7 1.0
OG D:SER72 3.0 8.9 1.0
OG C:SER72 3.0 8.8 1.0
O C:ILE68 3.0 9.8 1.0
O D:ILE68 3.0 9.8 1.0
CB D:SER72 3.4 10.1 1.0
CB C:SER72 3.4 9.4 1.0
O C:HOH502 3.6 9.6 0.5
N C:ILE68 3.6 8.9 1.0
N D:ILE68 3.6 9.1 1.0
O C:HOH502 3.7 8.1 0.5
CD D:GLU48 3.8 13.5 1.0
CD C:GLU48 3.8 14.0 1.0
C C:ILE68 3.9 8.1 1.0
C D:ILE68 4.0 9.3 1.0
CA D:GLY67 4.1 10.2 1.0
CA C:GLY67 4.1 9.9 1.0
C D:GLY67 4.2 9.8 1.0
C C:GLY67 4.2 10.1 1.0
CA C:ILE68 4.3 7.9 1.0
CA D:ILE68 4.3 8.9 1.0
CG D:GLU48 4.3 14.2 1.0
CG C:GLU48 4.4 13.2 1.0
CB C:ILE68 4.7 10.0 1.0
CB D:ILE68 4.7 8.7 1.0
CA D:SER72 4.8 8.4 1.0
O D:THR66 4.8 11.3 1.0
OE1 D:GLU48 4.8 14.5 1.0
CA C:SER72 4.8 7.8 1.0
OE1 C:GLU48 4.8 14.8 1.0
O C:THR66 4.8 10.7 1.0
N D:SER72 4.9 8.1 1.0
N C:SER72 5.0 7.0 1.0

Sodium binding site 3 out of 3 in 5our

Go back to Sodium Binding Sites List in 5our
Sodium binding site 3 out of 3 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A.


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 2,2'-Anhydrouridine at 1.34 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:18.2
occ:1.00
OE2 F:GLU48 2.7 12.1 1.0
OE2 E:GLU48 2.8 13.1 1.0
OG F:SER72 2.9 7.5 1.0
O E:ILE68 3.0 8.7 1.0
OG E:SER72 3.0 9.9 1.0
O F:ILE68 3.0 8.0 1.0
CB F:SER72 3.4 8.3 1.0
CB E:SER72 3.4 9.5 1.0
N E:ILE68 3.6 8.0 1.0
O F:HOH499 3.6 8.5 0.6
N F:ILE68 3.6 7.7 1.0
O F:HOH499 3.6 4.7 0.5
CD F:GLU48 3.8 12.3 1.0
CD E:GLU48 3.9 12.6 1.0
C E:ILE68 3.9 7.2 1.0
C F:ILE68 4.0 7.8 1.0
CA E:GLY67 4.1 9.0 1.0
CA F:GLY67 4.1 9.1 1.0
C E:GLY67 4.1 8.7 1.0
C F:GLY67 4.2 8.1 1.0
CA E:ILE68 4.3 7.2 1.0
CA F:ILE68 4.3 8.2 1.0
CG E:GLU48 4.4 12.0 1.0
CG F:GLU48 4.4 13.4 1.0
CB E:ILE68 4.7 8.0 1.0
CB F:ILE68 4.7 8.4 1.0
CA F:SER72 4.8 7.3 1.0
CA E:SER72 4.8 7.5 1.0
OE1 F:GLU48 4.8 12.9 1.0
O E:THR66 4.8 10.9 1.0
O F:THR66 4.8 10.2 1.0
OE1 E:GLU48 4.9 13.4 1.0
N F:SER72 5.0 6.6 1.0
N E:SER72 5.0 7.2 1.0

Reference:

I.I.Prokofev, V.V.Balaev, A.G.Gabdoulkhakov, C.Betzel, A.A.Lashkov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 2,2'-Anhydrouridine at 1.34 A. To Be Published.
Page generated: Tue Dec 15 11:25:56 2020

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