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Potassium in PDB 5lok: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution

Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution

All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, M.V.Dontsova, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.68 / 1.11
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.258, 71.772, 89.228, 69.35, 72.17, 85.78
R / Rfree (%) 11.4 / 13.6

Other elements in 5lok:

The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution (pdb code 5lok). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5lok

Go back to Potassium Binding Sites List in 5lok
Potassium binding site 1 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K302

b:11.4
occ:0.43
OE2 A:GLU48 2.7 10.0 1.0
OE2 B:GLU48 2.8 10.2 1.0
OG B:SER72 2.9 8.0 1.0
OG A:SER72 2.9 8.0 1.0
O A:ILE68 2.9 8.7 1.0
HB3 B:SER72 2.9 9.2 1.0
HB3 A:SER72 3.0 9.9 1.0
O B:ILE68 3.0 7.9 1.0
H B:ILE68 3.2 10.1 1.0
H A:ILE68 3.2 10.3 1.0
HA3 B:GLY67 3.3 11.1 1.0
HA3 A:GLY67 3.3 11.6 1.0
CB B:SER72 3.4 7.7 1.0
CB A:SER72 3.4 8.3 1.0
O B:HOH466 3.6 8.4 0.5
O B:HOH466 3.6 7.6 0.5
N A:ILE68 3.6 8.6 1.0
N B:ILE68 3.6 8.4 1.0
HB2 B:SER72 3.7 9.2 1.0
HB2 A:SER72 3.7 9.9 1.0
HG3 B:GLU48 3.8 13.7 1.0
CD A:GLU48 3.8 11.2 1.0
HG3 A:GLU48 3.8 13.7 1.0
CD B:GLU48 3.9 11.1 1.0
C B:ILE68 3.9 7.5 1.0
C A:ILE68 3.9 7.9 1.0
HB B:ILE68 4.1 10.1 1.0
CA A:GLY67 4.1 9.7 1.0
CA B:GLY67 4.1 9.3 1.0
HB A:ILE68 4.1 10.5 1.0
C A:GLY67 4.2 9.0 1.0
C B:GLY67 4.2 9.0 1.0
CA B:ILE68 4.3 8.1 1.0
CA A:ILE68 4.3 8.4 1.0
CG A:GLU48 4.3 11.4 1.0
CG B:GLU48 4.4 11.4 1.0
H B:SER72 4.4 8.3 1.0
HA2 A:GLY67 4.4 11.6 1.0
H A:SER72 4.4 9.1 1.0
HA2 B:GLY67 4.4 11.1 1.0
HB3 A:GLU48 4.5 15.5 1.0
CB B:ILE68 4.7 8.4 1.0
HB3 B:GLU48 4.7 14.9 1.0
CB A:ILE68 4.8 8.8 1.0
CA B:SER72 4.8 7.1 1.0
O A:THR66 4.8 10.0 1.0
CA A:SER72 4.8 8.0 1.0
O B:THR66 4.8 9.4 1.0
OE1 A:GLU48 4.8 12.4 1.0
OE1 B:GLU48 4.9 12.8 1.0
CB A:GLU48 4.9 12.9 1.0
N B:SER72 4.9 6.9 1.0
N A:SER72 5.0 7.5 1.0
HB2 A:GLU48 5.0 15.5 1.0

Potassium binding site 2 out of 3 in 5lok

Go back to Potassium Binding Sites List in 5lok
Potassium binding site 2 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K302

b:13.3
occ:0.45
OE2 D:GLU48 2.8 12.6 1.0
OE2 C:GLU48 2.8 12.1 1.0
OG D:SER72 2.9 10.3 1.0
OG C:SER72 2.9 9.6 1.0
O C:ILE68 2.9 9.3 1.0
HB3 C:SER72 2.9 11.9 1.0
O D:ILE68 2.9 10.0 1.0
HB3 D:SER72 3.0 12.3 1.0
H C:ILE68 3.2 12.2 1.0
H D:ILE68 3.2 12.0 1.0
HA3 D:GLY67 3.3 13.3 1.0
HA3 C:GLY67 3.4 13.1 1.0
CB C:SER72 3.4 9.9 1.0
CB D:SER72 3.4 10.2 1.0
N C:ILE68 3.6 10.2 1.0
N D:ILE68 3.6 10.0 1.0
O C:HOH488 3.6 9.0 0.5
O C:HOH488 3.7 9.1 0.5
HB2 C:SER72 3.7 11.9 1.0
HB2 D:SER72 3.7 12.3 1.0
HG3 D:GLU48 3.8 17.1 1.0
CD D:GLU48 3.9 13.2 1.0
HG3 C:GLU48 3.9 16.4 1.0
CD C:GLU48 3.9 12.8 1.0
C D:ILE68 3.9 9.0 1.0
C C:ILE68 3.9 8.8 1.0
CA D:GLY67 4.1 11.1 1.0
HB D:ILE68 4.1 11.7 1.0
HB C:ILE68 4.1 11.7 1.0
CA C:GLY67 4.1 10.9 1.0
C D:GLY67 4.2 10.1 1.0
C C:GLY67 4.2 10.1 1.0
CA C:ILE68 4.3 9.5 1.0
CA D:ILE68 4.3 9.9 1.0
CG D:GLU48 4.3 14.3 1.0
CG C:GLU48 4.4 13.7 1.0
HA2 D:GLY67 4.4 13.3 1.0
H D:SER72 4.4 10.4 1.0
H C:SER72 4.4 9.9 1.0
HA2 C:GLY67 4.4 13.1 1.0
HB3 C:GLU48 4.6 16.8 1.0
HB3 D:GLU48 4.7 18.5 1.0
CB D:ILE68 4.7 9.8 1.0
CB C:ILE68 4.7 9.7 1.0
CA D:SER72 4.8 9.1 1.0
CA C:SER72 4.8 9.2 1.0
O D:THR66 4.8 11.2 1.0
O C:THR66 4.8 11.1 1.0
OE1 D:GLU48 4.8 14.3 1.0
OE1 C:GLU48 4.9 14.3 1.0
N D:SER72 5.0 8.7 1.0
N C:SER72 5.0 8.3 1.0
CB C:GLU48 5.0 14.0 1.0

Potassium binding site 3 out of 3 in 5lok

Go back to Potassium Binding Sites List in 5lok
Potassium binding site 3 out of 3 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K304

b:12.0
occ:0.43
OE2 F:GLU48 2.8 11.8 1.0
OE2 E:GLU48 2.8 12.1 1.0
OG E:SER72 2.9 9.6 1.0
O F:ILE68 2.9 10.0 1.0
OG F:SER72 2.9 9.7 1.0
O E:ILE68 2.9 9.7 1.0
HB3 F:SER72 2.9 11.7 1.0
HB3 E:SER72 3.0 11.1 1.0
H F:ILE68 3.2 12.5 1.0
H E:ILE68 3.2 11.2 1.0
HA3 F:GLY67 3.3 12.8 1.0
HA3 E:GLY67 3.4 12.3 1.0
CB F:SER72 3.4 9.8 1.0
CB E:SER72 3.4 9.3 1.0
O F:HOH464 3.6 9.9 0.6
O F:HOH464 3.6 8.8 0.4
N F:ILE68 3.6 10.4 1.0
N E:ILE68 3.6 9.3 1.0
HB2 F:SER72 3.7 11.7 1.0
HB2 E:SER72 3.7 11.1 1.0
CD F:GLU48 3.9 13.3 1.0
HG3 F:GLU48 3.9 16.4 1.0
C F:ILE68 3.9 9.3 1.0
CD E:GLU48 3.9 13.0 1.0
C E:ILE68 3.9 9.1 1.0
HG3 E:GLU48 3.9 15.9 1.0
HB F:ILE68 4.1 12.5 1.0
HB E:ILE68 4.1 11.7 1.0
CA F:GLY67 4.1 10.7 1.0
CA E:GLY67 4.1 10.3 1.0
C F:GLY67 4.2 10.7 1.0
C E:GLY67 4.2 9.9 1.0
CA F:ILE68 4.2 10.2 1.0
CA E:ILE68 4.3 9.5 1.0
H F:SER72 4.3 10.7 1.0
CG F:GLU48 4.4 13.7 1.0
H E:SER72 4.4 10.2 1.0
CG E:GLU48 4.4 13.2 1.0
HA2 F:GLY67 4.4 12.8 1.0
HA2 E:GLY67 4.5 12.3 1.0
CB F:ILE68 4.7 10.4 1.0
HB3 E:GLU48 4.7 17.1 1.0
HB3 F:GLU48 4.7 17.9 1.0
CB E:ILE68 4.7 9.7 1.0
CA F:SER72 4.7 9.0 1.0
CA E:SER72 4.7 8.7 1.0
O F:THR66 4.8 11.5 1.0
O E:THR66 4.8 10.7 1.0
OE1 F:GLU48 4.9 14.8 1.0
OE1 E:GLU48 4.9 14.4 1.0
N F:SER72 4.9 8.9 1.0
N E:SER72 5.0 8.5 1.0

Reference:

I.I.Prokofev, A.G.Gabdoulkhakov, A.A.Lashkov, V.V.Balaev, C.Betzel, A.M.Mikhailov. X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution To Be Published.
Page generated: Mon Aug 12 14:14:53 2024

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