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Potassium in PDB 1rxs: E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex

Enzymatic activity of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex

All present enzymatic activity of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex:
2.4.2.3;

Protein crystallography data

The structure of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex, PDB code: 1rxs was solved by T.T.Caradoc-Davies, S.M.Cutfield, I.L.Lamont, J.F.Cutfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.75 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 160.958, 98.212, 242.729, 90.00, 109.09, 90.00
R / Rfree (%) 17.6 / 21.8

Other elements in 1rxs:

The structure of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex also contains other interesting chemical elements:

Vanadium (V) 60 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex (pdb code 1rxs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex, PDB code: 1rxs:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in 1rxs

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Potassium binding site 1 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K4011

b:34.5
occ:1.00
OE2 a:GLU2049 2.7 15.6 1.0
OE1 A:GLU3049 2.8 21.3 1.0
OG A:SER3073 2.8 11.4 1.0
O A:ILE3069 2.9 9.8 1.0
O a:ILE2069 3.0 10.5 1.0
OG a:SER2073 3.1 11.1 1.0
N A:ILE3069 3.4 9.3 1.0
CB A:SER3073 3.6 11.1 1.0
CB a:SER2073 3.7 10.5 1.0
N a:ILE2069 3.8 9.7 1.0
CD a:GLU2049 3.8 14.8 1.0
C A:ILE3069 3.8 9.5 1.0
CD A:GLU3049 3.9 19.7 1.0
C a:ILE2069 4.0 10.0 1.0
C A:GLY3068 4.1 9.5 1.0
CA A:ILE3069 4.1 9.3 1.0
CA A:GLY3068 4.2 9.3 1.0
CG a:GLU2049 4.4 13.2 1.0
CG A:GLU3049 4.4 17.3 1.0
CA a:ILE2069 4.4 9.3 1.0
CA a:GLY2068 4.4 10.5 1.0
C a:GLY2068 4.4 10.3 1.0
CB A:ILE3069 4.6 9.3 1.0
O A:THR3067 4.6 10.6 1.0
CB a:ILE2069 4.7 8.9 1.0
OE1 a:GLU2049 4.8 15.8 1.0
CA A:SER3073 4.9 11.3 1.0
N A:SER3073 4.9 10.7 1.0
OE2 A:GLU3049 4.9 20.6 1.0
O a:THR2067 4.9 11.8 1.0
N A:GLY3070 5.0 9.9 1.0
CA a:SER2073 5.0 10.8 1.0

Potassium binding site 2 out of 15 in 1rxs

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Potassium binding site 2 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K4021

b:36.2
occ:1.00
OE1 B:GLU1049 2.7 17.9 1.0
OE2 b:GLU2049 2.8 15.8 1.0
O B:ILE1069 2.8 9.6 1.0
OG b:SER2073 2.9 10.7 1.0
O b:ILE2069 2.9 10.5 1.0
OG B:SER1073 3.1 11.4 1.0
CB B:SER1073 3.5 10.3 1.0
CB b:SER2073 3.6 10.0 1.0
N B:ILE1069 3.6 9.3 1.0
N b:ILE2069 3.6 9.9 1.0
C B:ILE1069 3.8 9.2 1.0
CD B:GLU1049 3.8 16.6 1.0
CD b:GLU2049 3.9 14.7 1.0
C b:ILE2069 3.9 9.9 1.0
CA b:GLY2068 4.2 10.6 1.0
CA B:ILE1069 4.2 8.8 1.0
C b:GLY2068 4.2 10.4 1.0
C B:GLY1068 4.2 10.0 1.0
CA b:ILE2069 4.2 9.6 1.0
CG b:GLU2049 4.3 13.3 1.0
CA B:GLY1068 4.3 10.0 1.0
CG B:GLU1049 4.3 14.7 1.0
CB b:ILE2069 4.6 9.2 1.0
CB B:ILE1069 4.7 8.7 1.0
O b:THR2067 4.8 11.9 1.0
CA B:SER1073 4.8 10.4 1.0
O B:THR1067 4.8 11.4 1.0
CA b:SER2073 4.8 10.7 1.0
OE2 B:GLU1049 4.9 16.2 1.0
OE1 b:GLU2049 4.9 15.5 1.0
N B:SER1073 4.9 10.0 1.0
N b:SER2073 4.9 10.3 1.0
N B:GLY1070 5.0 9.1 1.0
CB b:GLU2049 5.0 13.2 1.0

Potassium binding site 3 out of 15 in 1rxs

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Potassium binding site 3 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K4031

b:40.1
occ:1.00
OE1 C:GLU1049 2.8 17.9 1.0
OE2 c:GLU2049 2.8 15.6 1.0
O c:ILE2069 2.9 10.5 1.0
O C:ILE1069 2.9 9.4 1.0
OG c:SER2073 2.9 11.0 1.0
OG C:SER1073 3.0 11.3 1.0
CB C:SER1073 3.5 10.5 1.0
N c:ILE2069 3.6 9.6 1.0
CB c:SER2073 3.6 10.2 1.0
N C:ILE1069 3.6 9.5 1.0
C c:ILE2069 3.9 9.8 1.0
CD c:GLU2049 3.9 14.9 1.0
C C:ILE1069 3.9 9.1 1.0
CD C:GLU1049 3.9 16.3 1.0
C c:GLY2068 4.2 10.2 1.0
CA c:GLY2068 4.2 10.7 1.0
CA C:ILE1069 4.2 9.0 1.0
CA c:ILE2069 4.2 9.2 1.0
C C:GLY1068 4.3 10.1 1.0
CG c:GLU2049 4.3 13.4 1.0
CA C:GLY1068 4.3 10.4 1.0
CG C:GLU1049 4.4 14.8 1.0
CB c:ILE2069 4.6 9.0 1.0
CB C:ILE1069 4.6 8.8 1.0
CA C:SER1073 4.8 10.5 1.0
O c:THR2067 4.8 11.9 1.0
CA c:SER2073 4.8 10.7 1.0
O C:THR1067 4.9 11.4 1.0
OE1 c:GLU2049 4.9 15.9 1.0
N c:SER2073 4.9 10.3 1.0
N C:SER1073 4.9 10.3 1.0
OE2 C:GLU1049 4.9 15.9 1.0
N c:GLY2070 5.0 9.8 1.0

Potassium binding site 4 out of 15 in 1rxs

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Potassium binding site 4 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K4041

b:64.3
occ:1.00
OE1 d:GLU3049 2.8 21.6 1.0
O D:ILE1069 2.9 9.5 1.0
OE1 D:GLU1049 2.9 17.8 1.0
O d:ILE3069 2.9 9.7 1.0
OG d:SER3073 2.9 11.2 1.0
OG D:SER1073 3.2 11.2 1.0
N d:ILE3069 3.6 9.1 1.0
CB d:SER3073 3.6 10.9 1.0
CB D:SER1073 3.7 10.2 1.0
N D:ILE1069 3.7 9.5 1.0
C D:ILE1069 3.9 9.1 1.0
C d:ILE3069 3.9 9.4 1.0
CD d:GLU3049 3.9 19.8 1.0
CD D:GLU1049 4.0 16.4 1.0
CA d:ILE3069 4.2 9.3 1.0
CA D:ILE1069 4.2 8.8 1.0
C d:GLY3068 4.3 9.4 1.0
CA d:GLY3068 4.4 9.4 1.0
C D:GLY1068 4.4 10.2 1.0
CG d:GLU3049 4.4 17.2 1.0
CG D:GLU1049 4.5 14.8 1.0
CA D:GLY1068 4.5 10.2 1.0
CB D:ILE1069 4.6 8.6 1.0
CB d:ILE3069 4.7 9.5 1.0
O d:THR3067 4.8 10.8 1.0
CA d:SER3073 4.8 11.1 1.0
N d:SER3073 4.9 10.6 1.0
OE2 d:GLU3049 5.0 20.4 1.0
CA D:SER1073 5.0 10.4 1.0
OE2 D:GLU1049 5.0 16.3 1.0

Potassium binding site 5 out of 15 in 1rxs

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Potassium binding site 5 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K4051

b:49.6
occ:1.00
O e:ILE2069 2.7 10.1 1.0
OE1 E:GLU1049 2.8 17.9 1.0
O E:ILE1069 2.9 9.3 1.0
OE2 e:GLU2049 2.9 15.6 1.0
OG e:SER2073 2.9 11.1 1.0
OG E:SER1073 3.0 11.1 1.0
CB E:SER1073 3.5 10.3 1.0
N e:ILE2069 3.5 9.8 1.0
CB e:SER2073 3.6 10.4 1.0
C e:ILE2069 3.7 9.7 1.0
N E:ILE1069 3.8 9.2 1.0
C E:ILE1069 3.9 9.1 1.0
CD E:GLU1049 3.9 16.4 1.0
CD e:GLU2049 4.0 14.8 1.0
CA e:ILE2069 4.1 9.4 1.0
C e:GLY2068 4.2 10.4 1.0
CA e:GLY2068 4.3 10.6 1.0
CA E:ILE1069 4.3 8.8 1.0
C E:GLY1068 4.4 9.9 1.0
CG e:GLU2049 4.4 13.2 1.0
CB e:ILE2069 4.5 9.2 1.0
CA E:GLY1068 4.5 10.2 1.0
CG E:GLU1049 4.5 14.7 1.0
CB E:ILE1069 4.7 8.6 1.0
CA E:SER1073 4.7 10.5 1.0
N E:SER1073 4.8 10.2 1.0
O e:THR2067 4.8 11.8 1.0
N e:GLY2070 4.8 9.8 1.0
CA e:SER2073 4.9 10.7 1.0
N e:SER2073 4.9 10.4 1.0
O E:THR1067 4.9 11.5 1.0
OE2 E:GLU1049 4.9 16.4 1.0
OE1 e:GLU2049 5.0 15.7 1.0

Potassium binding site 6 out of 15 in 1rxs

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Potassium binding site 6 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:K4061

b:47.2
occ:1.00
O R:ILE1069 2.8 9.6 1.0
OE1 R:GLU1049 2.8 18.0 1.0
OE1 F:GLU1049 2.9 18.1 1.0
O F:ILE1069 2.9 9.8 1.0
OG R:SER1073 3.0 11.3 1.0
OG F:SER1073 3.1 11.2 1.0
N R:ILE1069 3.5 9.3 1.0
CB R:SER1073 3.5 10.2 1.0
CB F:SER1073 3.6 10.1 1.0
N F:ILE1069 3.7 9.2 1.0
C R:ILE1069 3.8 9.2 1.0
C F:ILE1069 3.9 9.1 1.0
CD R:GLU1049 3.9 16.3 1.0
CD F:GLU1049 4.0 16.5 1.0
CA R:ILE1069 4.1 8.9 1.0
C R:GLY1068 4.2 10.1 1.0
CA F:ILE1069 4.2 8.8 1.0
CA R:GLY1068 4.3 10.1 1.0
C F:GLY1068 4.4 10.1 1.0
CG R:GLU1049 4.4 14.8 1.0
CG F:GLU1049 4.5 14.6 1.0
CA F:GLY1068 4.5 10.2 1.0
CB F:ILE1069 4.6 8.6 1.0
CB R:ILE1069 4.6 8.7 1.0
CA R:SER1073 4.8 10.5 1.0
O R:THR1067 4.8 11.7 1.0
N R:SER1073 4.9 10.3 1.0
CA F:SER1073 4.9 10.4 1.0
N R:GLY1070 5.0 8.9 1.0
OE2 R:GLU1049 5.0 16.2 1.0
OE2 F:GLU1049 5.0 16.6 1.0
N F:SER1073 5.0 10.2 1.0

Potassium binding site 7 out of 15 in 1rxs

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Potassium binding site 7 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K4071

b:40.2
occ:1.00
OE2 G:GLU2049 2.7 15.6 1.0
O P:ILE2069 2.8 10.3 1.0
OE2 P:GLU2049 2.8 15.4 1.0
OG G:SER2073 2.9 10.9 1.0
OG P:SER2073 2.9 10.9 1.0
O G:ILE2069 3.0 10.5 1.0
CB G:SER2073 3.5 10.2 1.0
N P:ILE2069 3.5 9.8 1.0
CB P:SER2073 3.6 10.3 1.0
N G:ILE2069 3.7 9.7 1.0
C P:ILE2069 3.7 9.8 1.0
CD G:GLU2049 3.8 14.9 1.0
CD P:GLU2049 3.9 14.8 1.0
C G:ILE2069 4.0 9.8 1.0
CA P:ILE2069 4.1 9.3 1.0
C P:GLY2068 4.2 10.6 1.0
CA P:GLY2068 4.2 10.7 1.0
CG G:GLU2049 4.3 13.3 1.0
C G:GLY2068 4.3 10.2 1.0
CA G:GLY2068 4.3 10.6 1.0
CA G:ILE2069 4.3 9.4 1.0
CG P:GLU2049 4.4 13.2 1.0
CB P:ILE2069 4.5 8.9 1.0
O G:THR2067 4.7 11.9 1.0
CA G:SER2073 4.7 10.6 1.0
CB G:ILE2069 4.7 9.1 1.0
OE1 G:GLU2049 4.8 15.9 1.0
N G:SER2073 4.8 10.2 1.0
O P:THR2067 4.8 11.8 1.0
CA P:SER2073 4.9 10.7 1.0
OE1 P:GLU2049 4.9 16.0 1.0
N P:GLY2070 4.9 9.9 1.0
N P:SER2073 5.0 10.2 1.0

Potassium binding site 8 out of 15 in 1rxs

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Potassium binding site 8 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
h:K4081

b:51.7
occ:1.00
OE1 H:GLU1049 2.7 17.9 1.0
OE2 h:GLU2049 2.8 15.5 1.0
O h:ILE2069 2.9 10.4 1.0
OG h:SER2073 2.9 11.1 1.0
O H:ILE1069 2.9 9.4 1.0
OG H:SER1073 3.1 11.3 1.0
N h:ILE2069 3.5 9.9 1.0
CB H:SER1073 3.5 10.2 1.0
CB h:SER2073 3.5 10.5 1.0
N H:ILE1069 3.6 9.3 1.0
C h:ILE2069 3.8 9.8 1.0
CD H:GLU1049 3.8 16.3 1.0
CD h:GLU2049 3.9 14.7 1.0
C H:ILE1069 3.9 9.0 1.0
CA h:ILE2069 4.1 9.5 1.0
C h:GLY2068 4.2 10.4 1.0
CA h:GLY2068 4.2 10.5 1.0
CA H:ILE1069 4.2 8.9 1.0
C H:GLY1068 4.2 10.1 1.0
CG h:GLU2049 4.3 13.2 1.0
CA H:GLY1068 4.3 10.4 1.0
CG H:GLU1049 4.4 14.7 1.0
CB h:ILE2069 4.6 9.1 1.0
CB H:ILE1069 4.7 8.8 1.0
O h:THR2067 4.7 11.9 1.0
CA h:SER2073 4.8 10.8 1.0
O H:THR1067 4.8 11.4 1.0
OE2 H:GLU1049 4.8 16.2 1.0
CA H:SER1073 4.8 10.5 1.0
N h:SER2073 4.9 10.6 1.0
OE1 h:GLU2049 4.9 15.7 1.0
N h:GLY2070 4.9 9.9 1.0
N H:SER1073 5.0 10.4 1.0

Potassium binding site 9 out of 15 in 1rxs

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Potassium binding site 9 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K4091

b:45.4
occ:1.00
OE1 i:GLU1049 2.7 17.9 1.0
OG i:SER1073 2.8 11.0 1.0
O i:ILE1069 2.8 9.3 1.0
OE2 I:GLU2049 2.9 15.8 1.0
O I:ILE2069 3.0 10.4 1.0
OG I:SER2073 3.1 10.9 1.0
CB i:SER1073 3.4 10.2 1.0
N i:ILE1069 3.5 9.4 1.0
CB I:SER2073 3.7 10.5 1.0
N I:ILE2069 3.7 9.7 1.0
C i:ILE1069 3.8 9.0 1.0
CD i:GLU1049 3.9 16.4 1.0
CD I:GLU2049 3.9 14.8 1.0
C I:ILE2069 4.0 9.8 1.0
C i:GLY1068 4.1 10.2 1.0
CA i:ILE1069 4.1 8.8 1.0
CA i:GLY1068 4.2 10.3 1.0
CG i:GLU1049 4.3 14.9 1.0
CA I:ILE2069 4.3 9.4 1.0
CG I:GLU2049 4.4 13.1 1.0
C I:GLY2068 4.4 10.3 1.0
CA I:GLY2068 4.5 10.5 1.0
CB i:ILE1069 4.6 8.8 1.0
CB I:ILE2069 4.7 9.0 1.0
O i:THR1067 4.7 11.6 1.0
CA i:SER1073 4.7 10.3 1.0
N i:SER1073 4.9 10.2 1.0
OE1 I:GLU2049 4.9 15.5 1.0
N i:GLY1070 4.9 8.9 1.0
OE2 i:GLU1049 4.9 16.3 1.0
CA I:SER2073 5.0 10.7 1.0
O I:THR2067 5.0 11.6 1.0
N I:SER2073 5.0 10.3 1.0

Potassium binding site 10 out of 15 in 1rxs

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Potassium binding site 10 out of 15 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K4101

b:32.8
occ:1.00
OE1 J:GLU1049 2.6 17.9 1.0
O j:ILE2069 2.8 10.2 1.0
OE2 j:GLU2049 2.9 15.6 1.0
OG J:SER1073 2.9 11.1 1.0
O J:ILE1069 3.1 9.6 1.0
OG j:SER2073 3.1 11.1 1.0
CB J:SER1073 3.4 10.0 1.0
N j:ILE2069 3.5 9.9 1.0
N J:ILE1069 3.7 9.4 1.0
CB j:SER2073 3.7 10.3 1.0
CD J:GLU1049 3.7 16.2 1.0
C j:ILE2069 3.8 9.8 1.0
CD j:GLU2049 3.9 15.0 1.0
C J:ILE1069 4.0 9.0 1.0
CA j:ILE2069 4.1 9.4 1.0
C j:GLY2068 4.2 10.4 1.0
CA j:GLY2068 4.3 10.5 1.0
CG J:GLU1049 4.3 14.6 1.0
C J:GLY1068 4.3 10.2 1.0
CG j:GLU2049 4.3 13.3 1.0
CA J:GLY1068 4.3 10.4 1.0
CA J:ILE1069 4.3 9.0 1.0
CB j:ILE2069 4.5 9.1 1.0
O J:THR1067 4.7 11.5 1.0
OE2 J:GLU1049 4.7 16.3 1.0
CA J:SER1073 4.8 10.3 1.0
CB J:ILE1069 4.8 8.9 1.0
O j:THR2067 4.8 12.0 1.0
N J:SER1073 4.9 10.1 1.0
N j:GLY2070 4.9 9.8 1.0
CA j:SER2073 4.9 10.8 1.0
OE1 j:GLU2049 5.0 15.9 1.0
CB J:GLU1049 5.0 13.9 1.0

Reference:

T.T.Caradoc-Davies, S.M.Cutfield, I.L.Lamont, J.F.Cutfield. Crystal Structures of Escherichia Coli Uridine Phosphorylase in Two Native and Three Complexed Forms Reveal Basis of Substrate Specificity, Induced Conformational Changes and Influence of Potassium J.Mol.Biol. V. 337 337 2004.
ISSN: ISSN 0022-2836
PubMed: 15003451
DOI: 10.1016/J.JMB.2004.01.039
Page generated: Sun Dec 13 23:01:16 2020

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