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Vanadium 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:

Potassium (K) 15 atoms

Vanadium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60;

Binding sites:

The binding sites of Vanadium 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 Vanadium atom.
In total 60 binding sites of Vanadium where determined in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex, PDB code: 1rxs:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Vanadium binding site 1 out of 60 in 1rxs

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Vanadium binding site 1 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V 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:V5011

b:78.6
occ:1.00
V5 A:V7O5011 0.0 78.6 1.0
O14 A:V7O5011 1.9 83.1 1.0
O12 A:V7O5011 1.9 79.1 1.0
O13 A:V7O5011 1.9 78.2 1.0
O14 B:V7O5012 2.9 78.3 1.0
O16 B:V7O5012 2.9 77.4 1.0
O19 B:V7O5012 2.9 76.3 1.0
V6 B:V7O5012 3.1 76.8 1.0
V6 A:V7O5011 3.3 83.5 1.0
V7 A:V7O5011 3.3 88.5 1.0
V7 B:V7O5012 3.4 78.2 1.0
O15 A:V7O5011 3.5 82.7 1.0
O18 A:V7O5011 3.5 84.8 1.0
ND1 A:HIS3179 3.6 16.4 1.0
CE1 A:HIS3179 4.1 17.4 1.0
O17 A:V7O5011 4.5 84.0 1.0
V5 B:V7O5012 4.6 73.1 1.0
O19 A:V7O5011 4.7 83.7 1.0
O17 B:V7O5012 4.7 78.5 1.0
O18 B:V7O5012 4.7 75.8 1.0
O16 A:V7O5011 4.7 84.4 1.0
CG A:HIS3179 4.8 14.7 1.0
O15 B:V7O5012 4.9 78.1 1.0

Vanadium binding site 2 out of 60 in 1rxs

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Vanadium binding site 2 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V5011

b:83.5
occ:1.00
V6 A:V7O5011 0.0 83.5 1.0
O14 A:V7O5011 1.9 83.1 1.0
O16 A:V7O5011 1.9 84.4 1.0
O15 A:V7O5011 1.9 82.7 1.0
O14 B:V7O5012 3.1 78.3 1.0
O12 B:V7O5012 3.2 75.3 1.0
V5 A:V7O5011 3.3 78.6 1.0
O12 A:V7O5011 3.3 79.1 1.0
V7 A:V7O5011 3.3 88.5 1.0
V5 B:V7O5012 3.5 73.1 1.0
O13 B:V7O5012 3.6 75.0 1.0
ND1 B:HIS1179 3.6 18.2 1.0
O19 A:V7O5011 3.6 83.7 1.0
V6 B:V7O5012 3.7 76.8 1.0
CE1 B:HIS1179 3.9 19.3 1.0
O17 A:V7O5011 4.1 84.0 1.0
O13 A:V7O5011 4.6 78.2 1.0
V7 B:V7O5012 4.7 78.2 1.0
O18 A:V7O5011 4.9 84.8 1.0
CG B:HIS1179 4.9 15.7 1.0

Vanadium binding site 3 out of 60 in 1rxs

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Vanadium binding site 3 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V5011

b:88.5
occ:1.00
V7 A:V7O5011 0.0 88.5 1.0
O14 A:V7O5011 1.9 83.1 1.0
O17 A:V7O5011 1.9 84.0 1.0
O19 A:V7O5011 1.9 83.7 1.0
O18 A:V7O5011 1.9 84.8 1.0
V6 A:V7O5011 3.3 83.5 1.0
V5 A:V7O5011 3.3 78.6 1.0
O16 A:V7O5011 3.5 84.4 1.0
O13 B:V7O5012 3.7 75.0 1.0
O13 A:V7O5011 3.7 78.2 1.0
O14 B:V7O5012 3.8 78.3 1.0
O17 B:V7O5012 3.8 78.5 1.0
O19 B:V7O5012 3.9 76.3 1.0
V7 B:V7O5012 4.0 78.2 1.0
V5 B:V7O5012 4.5 73.1 1.0
ND1 C:HIS1179 4.5 18.3 1.0
CE1 C:HIS1179 4.6 19.1 1.0
O12 A:V7O5011 4.8 79.1 1.0
O15 A:V7O5011 4.8 82.7 1.0

Vanadium binding site 4 out of 60 in 1rxs

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Vanadium binding site 4 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V5012

b:73.1
occ:1.00
V5 B:V7O5012 0.0 73.1 1.0
O12 B:V7O5012 1.9 75.3 1.0
O14 B:V7O5012 1.9 78.3 1.0
O13 B:V7O5012 1.9 75.0 1.0
O16 A:V7O5011 2.9 84.4 1.0
V7 B:V7O5012 3.1 78.2 1.0
V6 B:V7O5012 3.2 76.8 1.0
O15 B:V7O5012 3.4 78.1 1.0
O17 B:V7O5012 3.4 78.5 1.0
O15 A:V7O5011 3.4 82.7 1.0
V6 A:V7O5011 3.5 83.5 1.0
CD B:ARG1178 3.6 17.1 1.0
O14 A:V7O5011 3.7 83.1 1.0
O18 B:V7O5012 3.7 75.8 1.0
O17 A:V7O5011 3.8 84.0 1.0
CG B:ARG1178 4.2 12.8 1.0
NH1 A:ARG3178 4.3 20.9 1.0
CA B:HIS1179 4.4 12.5 1.0
V7 A:V7O5011 4.5 88.5 1.0
NH1 B:ARG1178 4.5 22.0 1.0
ND1 B:HIS1179 4.5 18.2 1.0
V5 A:V7O5011 4.6 78.6 1.0
N B:HIS1179 4.7 11.6 1.0
O16 B:V7O5012 4.8 77.4 1.0
NE B:ARG1178 4.8 21.4 1.0
O B:ARG1178 4.8 11.0 1.0
C B:ARG1178 4.9 10.8 1.0
O19 B:V7O5012 4.9 76.3 1.0
CB B:HIS1179 5.0 12.8 1.0

Vanadium binding site 5 out of 60 in 1rxs

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Vanadium binding site 5 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V5012

b:76.8
occ:1.00
V6 B:V7O5012 0.0 76.8 1.0
O15 B:V7O5012 1.9 78.1 1.0
O16 B:V7O5012 1.9 77.4 1.0
O14 B:V7O5012 1.9 78.3 1.0
O15 A:V7O5011 2.5 82.7 1.0
O12 A:V7O5011 2.7 79.1 1.0
V5 A:V7O5011 3.1 78.6 1.0
V5 B:V7O5012 3.2 73.1 1.0
V7 B:V7O5012 3.3 78.2 1.0
O12 B:V7O5012 3.4 75.3 1.0
O18 B:V7O5012 3.4 75.8 1.0
O14 A:V7O5011 3.6 83.1 1.0
V6 A:V7O5011 3.7 83.5 1.0
CD A:ARG3178 3.8 16.3 1.0
NH1 C:ARG1178 4.0 22.0 1.0
O19 B:V7O5012 4.2 76.3 1.0
CG A:ARG3178 4.4 12.8 1.0
NH1 A:ARG3178 4.7 20.9 1.0
CA A:HIS3179 4.7 12.1 1.0
O16 A:V7O5011 4.7 84.4 1.0
O A:ARG3178 4.8 10.4 1.0
O13 B:V7O5012 4.8 75.0 1.0
O17 B:V7O5012 4.9 78.5 1.0
ND1 A:HIS3179 4.9 16.4 1.0
O13 A:V7O5011 4.9 78.2 1.0
NE A:ARG3178 5.0 18.6 1.0

Vanadium binding site 6 out of 60 in 1rxs

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Vanadium binding site 6 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V5012

b:78.2
occ:1.00
V7 B:V7O5012 0.0 78.2 1.0
O18 B:V7O5012 1.9 75.8 1.0
O14 B:V7O5012 1.9 78.3 1.0
O17 B:V7O5012 1.9 78.5 1.0
O19 B:V7O5012 1.9 76.3 1.0
V5 B:V7O5012 3.1 73.1 1.0
V6 B:V7O5012 3.3 76.8 1.0
O16 B:V7O5012 3.3 77.4 1.0
V5 A:V7O5011 3.4 78.6 1.0
O14 A:V7O5011 3.5 83.1 1.0
O17 A:V7O5011 3.6 84.0 1.0
O13 B:V7O5012 3.9 75.0 1.0
O15 B:V7O5012 3.9 78.1 1.0
NH1 B:ARG1178 3.9 22.0 1.0
V7 A:V7O5011 4.0 88.5 1.0
CD C:ARG1178 4.2 17.3 1.0
ND1 C:HIS1179 4.2 18.3 1.0
O18 A:V7O5011 4.3 84.8 1.0
CA C:HIS1179 4.4 12.5 1.0
O13 A:V7O5011 4.7 78.2 1.0
V6 A:V7O5011 4.7 83.5 1.0
O12 A:V7O5011 4.7 79.1 1.0
O12 B:V7O5012 4.7 75.3 1.0
CG C:ARG1178 4.8 13.0 1.0
O15 A:V7O5011 4.8 82.7 1.0
N C:HIS1179 4.9 11.9 1.0
CB C:HIS1179 4.9 12.8 1.0
CZ B:ARG1178 4.9 22.8 1.0
CD B:ARG1178 4.9 17.1 1.0
NH1 C:ARG1178 5.0 22.0 1.0
O16 A:V7O5011 5.0 84.4 1.0

Vanadium binding site 7 out of 60 in 1rxs

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Vanadium binding site 7 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 7 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:V5013

b:64.8
occ:1.00
V5 b:V7O5013 0.0 64.8 1.0
O13 b:V7O5013 1.9 64.4 1.0
O14 b:V7O5013 1.9 67.6 1.0
O12 b:V7O5013 1.9 63.6 1.0
O15 b:V7O5013 3.2 67.6 1.0
V6 b:V7O5013 3.3 66.3 1.0
V7 b:V7O5013 3.3 67.3 1.0
O13 c:V7O5014 3.3 89.2 1.0
O14 c:V7O5014 3.4 87.4 1.0
V5 c:V7O5014 3.4 87.9 1.0
O18 c:V7O5014 3.7 85.8 1.0
O18 b:V7O5013 3.9 66.0 1.0
CD a:ARG2178 4.0 22.3 1.0
NH1 b:ARG2178 4.0 28.3 1.0
V7 c:V7O5014 4.2 88.1 1.0
O17 b:V7O5013 4.2 68.1 1.0
CG a:ARG2178 4.4 17.6 1.0
O16 b:V7O5013 4.6 64.5 1.0
CA a:HIS2179 4.7 16.2 1.0
NH1 a:ARG2178 4.7 28.7 1.0
ND1 a:HIS2179 4.8 22.5 1.0
O19 b:V7O5013 4.8 69.3 1.0
V6 c:V7O5014 4.8 86.0 1.0

Vanadium binding site 8 out of 60 in 1rxs

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Vanadium binding site 8 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 8 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:V5013

b:66.3
occ:1.00
V6 b:V7O5013 0.0 66.3 1.0
O15 b:V7O5013 1.9 67.6 1.0
O14 b:V7O5013 1.9 67.6 1.0
O16 b:V7O5013 1.9 64.5 1.0
V5 b:V7O5013 3.3 64.8 1.0
V7 b:V7O5013 3.3 67.3 1.0
O14 c:V7O5014 3.3 87.4 1.0
O19 b:V7O5013 3.4 69.3 1.0
CD c:ARG2178 3.7 22.4 1.0
O18 c:V7O5014 3.7 85.8 1.0
O12 b:V7O5013 3.8 63.6 1.0
V7 c:V7O5014 3.8 88.1 1.0
V6 c:V7O5014 3.9 86.0 1.0
O19 c:V7O5014 4.0 87.8 1.0
CG c:ARG2178 4.2 17.6 1.0
NH1 a:ARG2178 4.3 28.7 1.0
CA c:HIS2179 4.3 16.3 1.0
O17 b:V7O5013 4.4 68.1 1.0
ND1 c:HIS2179 4.4 22.4 1.0
O13 b:V7O5013 4.6 64.4 1.0
NH1 c:ARG2178 4.7 28.5 1.0
N c:HIS2179 4.7 15.9 1.0
O16 c:V7O5014 4.8 86.5 1.0
CB c:HIS2179 4.8 16.9 1.0
O18 b:V7O5013 4.8 66.0 1.0
V5 c:V7O5014 4.8 87.9 1.0
C c:ARG2178 4.9 15.2 1.0
NE c:ARG2178 4.9 26.6 1.0
O c:ARG2178 5.0 15.3 1.0

Vanadium binding site 9 out of 60 in 1rxs

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Vanadium binding site 9 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 9 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:V5013

b:67.3
occ:1.00
V7 b:V7O5013 0.0 67.3 1.0
O17 b:V7O5013 1.9 68.1 1.0
O19 b:V7O5013 1.9 69.3 1.0
O18 b:V7O5013 1.9 66.0 1.0
O14 b:V7O5013 1.9 67.6 1.0
V6 c:V7O5014 3.2 86.0 1.0
O14 c:V7O5014 3.2 87.4 1.0
O13 b:V7O5013 3.3 64.4 1.0
V6 b:V7O5013 3.3 66.3 1.0
V5 b:V7O5013 3.3 64.8 1.0
O16 b:V7O5013 3.7 64.5 1.0
V5 c:V7O5014 3.7 87.9 1.0
NH1 c:ARG2178 3.7 28.5 1.0
O15 c:V7O5014 3.9 86.4 1.0
CD b:ARG2178 4.1 22.2 1.0
CA b:HIS2179 4.3 16.3 1.0
ND1 b:HIS2179 4.4 22.3 1.0
CG b:ARG2178 4.5 17.7 1.0
O15 b:V7O5013 4.7 67.6 1.0
N b:HIS2179 4.8 15.7 1.0
O12 b:V7O5013 4.8 63.6 1.0
CD c:ARG2178 4.8 22.4 1.0
CZ c:ARG2178 4.8 28.7 1.0
CB b:HIS2179 4.9 16.9 1.0
NH1 b:ARG2178 4.9 28.3 1.0
V7 c:V7O5014 4.9 88.1 1.0

Vanadium binding site 10 out of 60 in 1rxs

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Vanadium binding site 10 out of 60 in the E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 10 of E. Coli Uridine Phosphorylase: 2'-Deoxyuridine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:V5014

b:87.9
occ:1.00
V5 c:V7O5014 0.0 87.9 1.0
O14 c:V7O5014 1.9 87.4 1.0
O13 c:V7O5014 1.9 89.2 1.0
O12 c:V7O5014 1.9 85.6 1.0
O13 b:V7O5013 2.4 64.4 1.0
O18 b:V7O5013 2.7 66.0 1.0
V7 c:V7O5014 3.1 88.1 1.0
V6 c:V7O5014 3.2 86.0 1.0
O15 c:V7O5014 3.3 86.4 1.0
O17 c:V7O5014 3.3 84.9 1.0
V5 b:V7O5013 3.4 64.8 1.0
O12 b:V7O5013 3.5 63.6 1.0
V7 b:V7O5013 3.7 67.3 1.0
O14 b:V7O5013 3.7 67.6 1.0
ND1 a:HIS2179 3.8 22.5 1.0
O18 c:V7O5014 4.1 85.8 1.0
CE1 a:HIS2179 4.1 23.5 1.0
O16 c:V7O5014 4.6 86.5 1.0
O19 b:V7O5013 4.7 69.3 1.0
O19 c:V7O5014 4.8 87.8 1.0
O15 b:V7O5013 4.8 67.6 1.0
V6 b:V7O5013 4.8 66.3 1.0
O16 b:V7O5013 4.9 64.5 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: Wed Dec 16 02:30:21 2020

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