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Fluorine in PDB 1pk9: Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate

Enzymatic activity of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate

All present enzymatic activity of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate:
2.4.2.1;

Protein crystallography data

The structure of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate, PDB code: 1pk9 was solved by E.M.Bennett, C.Li, P.W.Allan, W.B.Parker, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.000, 122.000, 241.900, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 26.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate (pdb code 1pk9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate, PDB code: 1pk9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1pk9

Go back to Fluorine Binding Sites List in 1pk9
Fluorine binding site 1 out of 3 in the Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:19.4
occ:1.00
F A:2FA306 0.0 19.4 1.0
C2 A:2FA306 1.3 19.4 1.0
N1 A:2FA306 2.2 19.7 1.0
N3 A:2FA306 2.3 18.3 1.0
C6 A:2FA306 3.5 19.4 1.0
C4 A:2FA306 3.5 19.0 1.0
CG A:MET180 3.5 14.6 1.0
O A:HOH356 3.5 35.6 1.0
CD2 A:PHE159 3.6 15.2 1.0
SD A:MET180 3.8 17.4 1.0
CA A:PHE159 4.0 15.8 1.0
CG1 A:VAL178 4.0 15.4 1.0
C5 A:2FA306 4.0 18.9 1.0
O A:GLU179 4.0 16.3 1.0
CG A:PHE159 4.3 15.7 1.0
CB A:ALA156 4.3 15.2 1.0
C A:GLU179 4.3 16.4 1.0
CE2 A:PHE159 4.3 16.7 1.0
CB A:PHE159 4.3 15.4 1.0
O A:HOH336 4.5 28.6 1.0
N6 A:2FA306 4.5 20.7 1.0
CA A:GLU179 4.5 15.8 1.0
O A:VAL178 4.6 15.2 1.0
C A:VAL178 4.7 15.5 1.0
N A:GLU179 4.8 15.1 1.0
N A:PHE159 4.8 17.2 1.0
N9 A:2FA306 4.8 19.1 1.0
O A:PHE159 4.8 17.8 1.0
CB A:MET180 4.9 14.9 1.0
C A:PHE159 4.9 17.4 1.0

Fluorine binding site 2 out of 3 in 1pk9

Go back to Fluorine Binding Sites List in 1pk9
Fluorine binding site 2 out of 3 in the Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F307

b:20.2
occ:1.00
F B:2FA307 0.0 20.2 1.0
C2 B:2FA307 1.3 20.8 1.0
N1 B:2FA307 2.2 20.3 1.0
N3 B:2FA307 2.3 20.1 1.0
O B:HOH402 3.3 31.6 1.0
C6 B:2FA307 3.5 21.3 1.0
C4 B:2FA307 3.5 20.9 1.0
CD2 B:PHE159 3.5 17.8 1.0
CG B:MET180 3.6 13.8 1.0
SD B:MET180 3.9 16.4 1.0
C5 B:2FA307 4.0 21.9 1.0
CA B:PHE159 4.0 18.0 1.0
CG1 B:VAL178 4.0 16.1 1.0
O B:GLU179 4.1 14.8 1.0
CE2 B:PHE159 4.2 17.7 1.0
CG B:PHE159 4.3 18.0 1.0
O B:HOH366 4.3 38.8 1.0
CB B:ALA156 4.3 12.4 1.0
CB B:PHE159 4.3 17.4 1.0
C B:GLU179 4.4 16.1 1.0
N6 B:2FA307 4.5 21.4 1.0
CA B:GLU179 4.6 16.1 1.0
O B:VAL178 4.6 15.8 1.0
N9 B:2FA307 4.8 21.6 1.0
C B:VAL178 4.8 16.0 1.0
N B:GLU179 4.8 15.6 1.0
O B:PHE159 4.8 17.6 1.0
N B:PHE159 4.8 17.2 1.0
C B:PHE159 4.9 19.2 1.0
O B:LEU158 5.0 16.4 1.0

Fluorine binding site 3 out of 3 in 1pk9

Go back to Fluorine Binding Sites List in 1pk9
Fluorine binding site 3 out of 3 in the Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of E. Coli Purine Nucleoside Phosphorylase Complexed with 2-Fluoroadenosine and Sulfate/Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F308

b:20.4
occ:1.00
F C:2FA308 0.0 20.4 1.0
C2 C:2FA308 1.3 18.8 1.0
N1 C:2FA308 2.2 17.6 1.0
N3 C:2FA308 2.3 16.9 1.0
CG C:MET180 3.3 13.6 1.0
O C:HOH326 3.4 27.6 1.0
C6 C:2FA308 3.5 17.9 1.0
C4 C:2FA308 3.5 17.4 1.0
SD C:MET180 3.7 17.4 1.0
CD2 C:PHE159 3.8 16.6 1.0
CG1 C:VAL178 3.8 15.2 1.0
CA C:PHE159 3.9 15.4 1.0
O C:GLU179 3.9 15.5 1.0
C5 C:2FA308 4.0 17.7 1.0
CB C:ALA156 4.1 13.9 1.0
C C:GLU179 4.2 15.7 1.0
O C:HOH333 4.3 25.1 1.0
CB C:PHE159 4.3 15.7 1.0
CG C:PHE159 4.3 16.8 1.0
O C:VAL178 4.4 16.0 1.0
CA C:GLU179 4.4 16.1 1.0
N6 C:2FA308 4.5 16.1 1.0
CE2 C:PHE159 4.6 18.1 1.0
C C:VAL178 4.6 16.7 1.0
N C:PHE159 4.6 15.9 1.0
N C:GLU179 4.6 16.3 1.0
O C:PHE159 4.7 16.3 1.0
N9 C:2FA308 4.8 18.0 1.0
CB C:MET180 4.8 13.2 1.0
O C:LEU158 4.8 16.7 1.0
C C:PHE159 4.8 16.3 1.0
CB C:VAL178 4.8 16.4 1.0
N C:MET180 4.9 14.4 1.0
C2' C:2FA308 5.0 16.3 1.0

Reference:

E.M.Bennett, C.Li, P.W.Allan, W.B.Parker, S.E.Ealick. Structural Basis For Substrate Specificity of Escherichia Coli Purine Nucleoside Phosphorylase. J.Biol.Chem. V. 278 47110 2003.
ISSN: ISSN 0021-9258
PubMed: 12937174
DOI: 10.1074/JBC.M304622200
Page generated: Mon Jul 14 11:31:26 2025

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