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Potassium in PDB 1rxu: E. Coli Uridine Phosphorylase: Thymidine Phosphate Complex

Enzymatic activity of E. Coli Uridine Phosphorylase: Thymidine Phosphate Complex

All present enzymatic activity of E. Coli Uridine Phosphorylase: Thymidine Phosphate Complex:
2.4.2.3;

Protein crystallography data

The structure of E. Coli Uridine Phosphorylase: Thymidine Phosphate Complex, PDB code: 1rxu 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) 25.00 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 156.244, 97.655, 161.453, 90.00, 118.23, 90.00
R / Rfree (%) 21.2 / 22.9

Potassium Binding Sites:

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

Potassium binding site 1 out of 9 in 1rxu

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Potassium binding site 1 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K3001

b:40.1
occ:1.00
OE2 B:GLU49 2.5 27.8 1.0
OE2 A:GLU49 2.7 27.8 1.0
O A:ILE69 2.8 12.9 1.0
OG A:SER73 2.9 13.4 1.0
OG B:SER73 2.9 13.5 1.0
O B:ILE69 3.0 12.9 1.0
CB B:SER73 3.5 12.8 1.0
N A:ILE69 3.6 13.2 1.0
CB A:SER73 3.6 12.8 1.0
N B:ILE69 3.7 13.1 1.0
CD B:GLU49 3.7 26.7 1.0
C A:ILE69 3.8 12.7 1.0
CD A:GLU49 3.9 26.6 1.0
C B:ILE69 4.0 12.6 1.0
C A:GLY68 4.1 13.6 1.0
CA A:ILE69 4.1 12.7 1.0
CA A:GLY68 4.2 13.6 1.0
C B:GLY68 4.3 13.6 1.0
CA B:ILE69 4.4 12.6 1.0
CA B:GLY68 4.4 13.7 1.0
CG B:GLU49 4.4 24.5 1.0
CG A:GLU49 4.5 24.4 1.0
CB A:ILE69 4.7 12.6 1.0
OE1 B:GLU49 4.7 27.3 1.0
O A:THR67 4.7 14.7 1.0
O B:THR67 4.7 14.7 1.0
CA B:SER73 4.8 12.9 1.0
OE1 A:GLU49 4.9 27.2 1.0
CA A:SER73 4.9 12.7 1.0
N B:SER73 4.9 12.8 1.0
N A:GLY70 4.9 12.5 1.0
CB B:ILE69 4.9 12.6 1.0
N A:SER73 4.9 12.7 1.0
O A:GLY68 4.9 14.0 1.0

Potassium binding site 2 out of 9 in 1rxu

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Potassium binding site 2 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K3002

b:38.0
occ:1.00
OE2 C:GLU49 2.5 27.7 1.0
OE2 D:GLU49 2.6 27.6 1.0
OG D:SER73 2.8 13.6 1.0
OG C:SER73 2.9 13.4 1.0
O D:ILE69 2.9 12.9 1.0
O C:ILE69 3.0 12.8 1.0
N D:ILE69 3.5 13.2 1.0
CB C:SER73 3.6 12.8 1.0
CB D:SER73 3.6 12.8 1.0
N C:ILE69 3.7 13.1 1.0
CD C:GLU49 3.7 26.6 1.0
CD D:GLU49 3.8 26.6 1.0
C D:ILE69 3.9 12.6 1.0
C C:ILE69 4.0 12.5 1.0
C D:GLY68 4.1 13.7 1.0
CA D:GLY68 4.2 13.7 1.0
CA D:ILE69 4.2 12.6 1.0
C C:GLY68 4.2 13.6 1.0
CA C:ILE69 4.3 12.6 1.0
CG D:GLU49 4.4 24.5 1.0
CA C:GLY68 4.4 13.6 1.0
CG C:GLU49 4.4 24.4 1.0
O D:THR67 4.6 14.6 1.0
OE1 C:GLU49 4.7 27.3 1.0
CB D:ILE69 4.7 12.6 1.0
O C:THR67 4.8 14.6 1.0
OE1 D:GLU49 4.8 27.3 1.0
CA C:SER73 4.9 12.8 1.0
CB C:ILE69 4.9 12.7 1.0
CA D:SER73 4.9 12.7 1.0
N C:SER73 4.9 12.8 1.0
O D:GLY68 5.0 14.1 1.0
N D:GLY70 5.0 12.4 1.0

Potassium binding site 3 out of 9 in 1rxu

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Potassium binding site 3 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K3003

b:54.9
occ:1.00
OE2 F:GLU49 2.7 27.8 1.0
O E:ILE69 2.7 12.7 1.0
OG F:SER73 2.8 13.6 1.0
OE2 E:GLU49 2.8 27.7 1.0
OG E:SER73 2.8 13.5 1.0
O F:ILE69 2.9 13.0 1.0
CB F:SER73 3.4 12.9 1.0
CB E:SER73 3.6 12.8 1.0
N E:ILE69 3.6 13.2 1.0
C E:ILE69 3.7 12.6 1.0
N F:ILE69 3.7 13.2 1.0
CD F:GLU49 3.9 26.6 1.0
C F:ILE69 3.9 12.7 1.0
CD E:GLU49 4.0 26.6 1.0
CA E:ILE69 4.2 12.7 1.0
C E:GLY68 4.2 13.7 1.0
C F:GLY68 4.3 13.8 1.0
CA F:ILE69 4.4 12.6 1.0
CA E:GLY68 4.4 13.7 1.0
CA F:GLY68 4.5 13.8 1.0
CG F:GLU49 4.5 24.4 1.0
CG E:GLU49 4.6 24.5 1.0
CA F:SER73 4.7 12.8 1.0
N F:SER73 4.7 12.7 1.0
O E:THR67 4.7 14.6 1.0
CB E:ILE69 4.7 12.5 1.0
O F:THR67 4.7 14.3 1.0
CA E:SER73 4.8 12.8 1.0
OE1 F:GLU49 4.8 27.1 1.0
N E:GLY70 4.9 12.4 1.0
N E:SER73 4.9 12.7 1.0
CB F:ILE69 4.9 12.5 1.0
OE1 E:GLU49 4.9 27.2 1.0
N F:GLY70 5.0 12.5 1.0

Potassium binding site 4 out of 9 in 1rxu

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Potassium binding site 4 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K3004

b:45.5
occ:1.00
O G:ILE69 2.8 12.9 1.0
OE2 G:GLU49 2.8 27.8 1.0
O H:ILE69 2.8 12.9 1.0
OG G:SER73 2.8 13.5 1.0
OE2 H:GLU49 2.8 27.7 1.0
OG H:SER73 2.9 13.5 1.0
CB G:SER73 3.6 12.9 1.0
CB H:SER73 3.7 12.8 1.0
N G:ILE69 3.7 13.0 1.0
N H:ILE69 3.7 13.1 1.0
C G:ILE69 3.7 12.6 1.0
C H:ILE69 3.8 12.6 1.0
CD G:GLU49 4.0 26.7 1.0
CD H:GLU49 4.0 26.6 1.0
CA G:ILE69 4.2 12.5 1.0
C G:GLY68 4.3 13.6 1.0
CA H:ILE69 4.3 12.5 1.0
C H:GLY68 4.4 13.7 1.0
CA G:GLY68 4.5 13.7 1.0
CA H:GLY68 4.6 13.8 1.0
CG G:GLU49 4.6 24.4 1.0
CG H:GLU49 4.7 24.5 1.0
CB G:ILE69 4.7 12.5 1.0
CB H:ILE69 4.7 12.4 1.0
O G:THR67 4.8 14.6 1.0
CA G:SER73 4.8 12.8 1.0
N G:SER73 4.8 12.7 1.0
O H:THR67 4.8 14.5 1.0
N G:GLY70 4.9 12.5 1.0
N H:SER73 4.9 12.7 1.0
CA H:SER73 4.9 12.8 1.0
OE1 G:GLU49 4.9 27.4 1.0
N H:GLY70 4.9 12.5 1.0
OE1 H:GLU49 5.0 27.2 1.0

Potassium binding site 5 out of 9 in 1rxu

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Potassium binding site 5 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K3005

b:49.6
occ:1.00
OE2 J:GLU49 2.6 27.6 1.0
O I:ILE69 2.7 12.8 1.0
OE2 I:GLU49 2.8 27.6 1.0
OG I:SER73 2.8 13.6 1.0
OG J:SER73 3.0 13.5 1.0
O J:ILE69 3.1 12.8 1.0
N I:ILE69 3.4 13.1 1.0
CB J:SER73 3.6 12.7 1.0
CB I:SER73 3.6 12.8 1.0
C I:ILE69 3.7 12.6 1.0
CD J:GLU49 3.8 26.6 1.0
N J:ILE69 3.9 13.0 1.0
CD I:GLU49 3.9 26.6 1.0
C I:GLY68 4.0 13.8 1.0
CA I:ILE69 4.0 12.6 1.0
C J:ILE69 4.1 12.6 1.0
CA I:GLY68 4.2 13.8 1.0
C J:GLY68 4.5 13.6 1.0
CG I:GLU49 4.5 24.4 1.0
CG J:GLU49 4.5 24.4 1.0
CA J:ILE69 4.5 12.6 1.0
CA J:GLY68 4.6 13.7 1.0
CB I:ILE69 4.6 12.4 1.0
O I:THR67 4.6 14.5 1.0
OE1 J:GLU49 4.7 27.3 1.0
CA J:SER73 4.8 12.7 1.0
N I:GLY70 4.8 12.5 1.0
N J:SER73 4.8 12.6 1.0
O I:GLY68 4.9 14.1 1.0
CA I:SER73 4.9 12.8 1.0
O J:THR67 4.9 14.6 1.0
OE1 I:GLU49 4.9 27.3 1.0
N I:SER73 4.9 12.7 1.0

Potassium binding site 6 out of 9 in 1rxu

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Potassium binding site 6 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:K3006

b:28.0
occ:1.00
OE2 K:GLU49 2.7 27.8 1.0
OE2 L:GLU49 2.7 27.9 1.0
O K:ILE69 2.8 12.8 1.0
OG K:SER73 2.8 13.5 1.0
O L:ILE69 2.9 12.8 1.0
OG L:SER73 3.0 13.6 1.0
N K:ILE69 3.5 13.2 1.0
CB K:SER73 3.5 12.6 1.0
CB L:SER73 3.7 12.7 1.0
N L:ILE69 3.7 13.0 1.0
C K:ILE69 3.7 12.5 1.0
CD K:GLU49 3.9 26.8 1.0
CD L:GLU49 3.9 26.7 1.0
C L:ILE69 3.9 12.5 1.0
C K:GLY68 4.0 13.9 1.0
CA K:ILE69 4.1 12.5 1.0
CA K:GLY68 4.2 13.8 1.0
C L:GLY68 4.3 13.6 1.0
CA L:ILE69 4.3 12.5 1.0
CG K:GLU49 4.5 24.4 1.0
CA L:GLY68 4.5 13.7 1.0
O K:THR67 4.5 14.5 1.0
CG L:GLU49 4.6 24.3 1.0
CB K:ILE69 4.7 12.6 1.0
CA K:SER73 4.8 12.7 1.0
OE1 L:GLU49 4.8 27.3 1.0
O L:THR67 4.8 14.4 1.0
CB L:ILE69 4.8 12.5 1.0
N K:GLY70 4.8 12.3 1.0
N K:SER73 4.9 12.6 1.0
OE1 K:GLU49 4.9 27.5 1.0
CA L:SER73 4.9 12.7 1.0
N L:SER73 4.9 12.6 1.0
O K:GLY68 4.9 14.3 1.0

Potassium binding site 7 out of 9 in 1rxu

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Potassium binding site 7 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:K3007

b:50.4
occ:1.00
OE2 M:GLU49 2.6 27.9 1.0
OE2 N:GLU49 2.6 27.7 1.0
OG M:SER73 2.9 13.3 1.0
OG N:SER73 2.9 13.5 1.0
O N:ILE69 3.0 12.9 1.0
O M:ILE69 3.0 13.0 1.0
CB M:SER73 3.5 12.8 1.0
CB N:SER73 3.7 12.8 1.0
N M:ILE69 3.7 13.0 1.0
N N:ILE69 3.7 13.1 1.0
CD M:GLU49 3.8 26.7 1.0
CD N:GLU49 3.8 26.5 1.0
C N:ILE69 3.9 12.7 1.0
C M:ILE69 3.9 12.6 1.0
C M:GLY68 4.2 13.6 1.0
C N:GLY68 4.3 13.6 1.0
CA N:ILE69 4.3 12.7 1.0
CA M:GLY68 4.3 13.8 1.0
CA M:ILE69 4.3 12.6 1.0
CG M:GLU49 4.4 24.4 1.0
CA N:GLY68 4.4 13.7 1.0
CG N:GLU49 4.5 24.4 1.0
O M:THR67 4.7 14.7 1.0
OE1 M:GLU49 4.7 27.2 1.0
OE1 N:GLU49 4.8 27.3 1.0
CA M:SER73 4.8 12.8 1.0
O N:THR67 4.8 14.5 1.0
CB N:ILE69 4.8 12.5 1.0
CB M:ILE69 4.9 12.5 1.0
N M:SER73 4.9 12.6 1.0
CA N:SER73 4.9 12.7 1.0
N N:SER73 5.0 12.6 1.0

Potassium binding site 8 out of 9 in 1rxu

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Potassium binding site 8 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:K3009

b:66.2
occ:1.00
OE2 P:GLU49 2.7 27.8 1.0
OE2 O:GLU49 2.7 27.8 1.0
O O:ILE69 2.8 12.9 1.0
OG O:SER73 2.9 13.7 1.0
OG P:SER73 2.9 13.5 1.0
O P:ILE69 2.9 12.9 1.0
CB P:SER73 3.6 12.8 1.0
CB O:SER73 3.6 12.8 1.0
N O:ILE69 3.6 13.1 1.0
N P:ILE69 3.7 13.0 1.0
C O:ILE69 3.8 12.7 1.0
CD P:GLU49 3.9 26.6 1.0
C P:ILE69 3.9 12.6 1.0
CD O:GLU49 3.9 26.6 1.0
C O:GLY68 4.2 13.6 1.0
CA O:ILE69 4.3 12.6 1.0
C P:GLY68 4.3 13.6 1.0
CA P:ILE69 4.3 12.6 1.0
CA O:GLY68 4.4 13.8 1.0
CA P:GLY68 4.4 13.7 1.0
CG O:GLU49 4.5 24.4 1.0
CG P:GLU49 4.5 24.4 1.0
O O:THR67 4.7 14.5 1.0
O P:THR67 4.8 14.5 1.0
CB O:ILE69 4.8 12.6 1.0
CA P:SER73 4.8 12.8 1.0
OE1 P:GLU49 4.8 27.3 1.0
CA O:SER73 4.8 12.7 1.0
N P:SER73 4.8 12.6 1.0
N O:SER73 4.8 12.6 1.0
CB P:ILE69 4.9 12.5 1.0
OE1 O:GLU49 4.9 27.2 1.0
N O:GLY70 4.9 12.6 1.0

Potassium binding site 9 out of 9 in 1rxu

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Potassium binding site 9 out of 9 in the E. Coli Uridine Phosphorylase: Thymidine 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: Thymidine Phosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:K3008

b:70.4
occ:1.00
OE2 Q:GLU49 2.7 27.8 1.0
O R:ILE69 2.7 12.8 1.0
OE2 R:GLU49 2.7 27.6 1.0
OG Q:SER73 2.8 13.4 1.0
OG R:SER73 2.8 13.7 1.0
O Q:ILE69 2.9 12.9 1.0
CB Q:SER73 3.5 12.8 1.0
N R:ILE69 3.5 13.2 1.0
CB R:SER73 3.6 12.8 1.0
N Q:ILE69 3.7 13.1 1.0
C R:ILE69 3.7 12.6 1.0
CD Q:GLU49 3.9 26.7 1.0
C Q:ILE69 3.9 12.7 1.0
CD R:GLU49 3.9 26.6 1.0
C R:GLY68 4.2 13.8 1.0
CA R:ILE69 4.2 12.6 1.0
C Q:GLY68 4.3 13.6 1.0
CA Q:ILE69 4.3 12.6 1.0
CA R:GLY68 4.4 13.8 1.0
CA Q:GLY68 4.4 13.7 1.0
CG Q:GLU49 4.5 24.3 1.0
CG R:GLU49 4.6 24.4 1.0
O Q:THR67 4.6 14.5 1.0
O R:THR67 4.7 14.6 1.0
CA Q:SER73 4.7 12.8 1.0
CB R:ILE69 4.8 12.7 1.0
N Q:SER73 4.8 12.7 1.0
CA R:SER73 4.8 12.8 1.0
OE1 Q:GLU49 4.8 27.4 1.0
N R:SER73 4.8 12.7 1.0
N R:GLY70 4.8 12.6 1.0
CB Q:ILE69 4.9 12.5 1.0
OE1 R:GLU49 4.9 27.3 1.0
N Q:GLY70 5.0 12.5 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: Mon Aug 12 05:18:48 2024

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