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Fluorine in PDB 7zsp: Human Purine Nucleoside Phosphorylase in Complex with Js-555

Enzymatic activity of Human Purine Nucleoside Phosphorylase in Complex with Js-555

All present enzymatic activity of Human Purine Nucleoside Phosphorylase in Complex with Js-555:
2.4.2.1;

Protein crystallography data

The structure of Human Purine Nucleoside Phosphorylase in Complex with Js-555, PDB code: 7zsp was solved by S.Djukic, P.Pachl, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 2.29
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 142.36, 142.36, 163.61, 90, 90, 120
R / Rfree (%) 21.4 / 25.6

Other elements in 7zsp:

The structure of Human Purine Nucleoside Phosphorylase in Complex with Js-555 also contains other interesting chemical elements:

Sodium (Na) 1 atom
Tungsten (W) 18 atoms
Tellurium (Te) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Purine Nucleoside Phosphorylase in Complex with Js-555 (pdb code 7zsp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Human Purine Nucleoside Phosphorylase in Complex with Js-555, PDB code: 7zsp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7zsp

Go back to Fluorine Binding Sites List in 7zsp
Fluorine binding site 1 out of 5 in the Human Purine Nucleoside Phosphorylase in Complex with Js-555


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Purine Nucleoside Phosphorylase in Complex with Js-555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:70.6
occ:1.00
 F1 A:JT3301 0.0 70.6 1.0
C20 A:JT3301 1.3 69.4 1.0
C15 A:JT3301 2.3 70.1 1.0
C19 A:JT3301 2.4 71.1 1.0
O5 A:JT3301 2.7 61.5 1.0
F2 A:JT3301 2.7 69.0 1.0
OH A:TYR88 3.0 65.8 1.0
C16 A:JT3301 3.6 73.8 1.0
C18 A:JT3301 3.6 70.8 1.0
C9 A:JT3301 3.6 55.9 1.0
CE1 A:HIS86 3.9 53.2 1.0
NE2 A:HIS86 4.1 57.2 1.0
C17 A:JT3301 4.1 74.9 1.0
C14 A:JT3301 4.1 56.4 1.0
CB A:SER33 4.1 108.7 1.0
C10 A:JT3301 4.3 57.0 1.0
CZ A:TYR88 4.4 57.2 1.0
C13 A:JT3301 4.4 55.7 1.0
C8 A:JT3301 4.4 57.1 1.0
OG A:SER33 4.4 113.8 1.0
F3 A:JT3301 4.7 81.4 1.0
ND1 A:HIS86 4.7 54.3 1.0
F5 A:JT3301 4.7 76.2 1.0
O1 A:JT3301 4.9 55.6 1.0
CD2 A:HIS86 4.9 59.2 1.0

Fluorine binding site 2 out of 5 in 7zsp

Go back to Fluorine Binding Sites List in 7zsp
Fluorine binding site 2 out of 5 in the Human Purine Nucleoside Phosphorylase in Complex with Js-555


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Purine Nucleoside Phosphorylase in Complex with Js-555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:69.0
occ:1.00
 F2 A:JT3301 0.0 69.0 1.0
C19 A:JT3301 1.3 71.1 1.0
C18 A:JT3301 2.3 70.8 1.0
C20 A:JT3301 2.4 69.4 1.0
F3 A:JT3301 2.7 81.4 1.0
F1 A:JT3301 2.7 70.6 1.0
C17 A:JT3301 3.6 74.9 1.0
C15 A:JT3301 3.6 70.1 1.0
CG2 A:VAL61 4.1 120.7 1.0
C16 A:JT3301 4.1 73.8 1.0
OH A:TYR88 4.3 65.8 1.0
CG1 A:VAL61 4.6 129.7 1.0
F4 A:JT3301 4.7 86.3 1.0
O5 A:JT3301 4.7 61.5 1.0

Fluorine binding site 3 out of 5 in 7zsp

Go back to Fluorine Binding Sites List in 7zsp
Fluorine binding site 3 out of 5 in the Human Purine Nucleoside Phosphorylase in Complex with Js-555


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Purine Nucleoside Phosphorylase in Complex with Js-555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:81.4
occ:1.00
 F3 A:JT3301 0.0 81.4 1.0
C18 A:JT3301 1.3 70.8 1.0
C19 A:JT3301 2.3 71.1 1.0
C17 A:JT3301 2.4 74.9 1.0
F2 A:JT3301 2.7 69.0 1.0
F4 A:JT3301 2.7 86.3 1.0
C20 A:JT3301 3.6 69.4 1.0
C16 A:JT3301 3.6 73.8 1.0
C15 A:JT3301 4.1 70.1 1.0
F1 A:JT3301 4.7 70.6 1.0
F5 A:JT3301 4.7 76.2 1.0
ND1 A:HIS257 4.8 94.0 1.0

Fluorine binding site 4 out of 5 in 7zsp

Go back to Fluorine Binding Sites List in 7zsp
Fluorine binding site 4 out of 5 in the Human Purine Nucleoside Phosphorylase in Complex with Js-555


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Purine Nucleoside Phosphorylase in Complex with Js-555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:86.3
occ:1.00
 F4 A:JT3301 0.0 86.3 1.0
C17 A:JT3301 1.3 74.9 1.0
C18 A:JT3301 2.3 70.8 1.0
C16 A:JT3301 2.4 73.8 1.0
F3 A:JT3301 2.7 81.4 1.0
F5 A:JT3301 2.7 76.2 1.0
ND1 A:HIS257 3.0 94.0 1.0
CG A:LEU261 3.6 93.7 1.0
CD1 A:LEU261 3.6 89.0 1.0
C19 A:JT3301 3.6 71.1 1.0
C15 A:JT3301 3.6 70.1 1.0
CD2 A:LEU261 3.7 94.0 1.0
CE1 A:HIS257 3.9 95.8 1.0
CG A:HIS257 3.9 89.8 1.0
CB A:HIS257 4.0 78.7 1.0
C20 A:JT3301 4.1 69.4 1.0
O A:HIS257 4.2 89.1 1.0
OG A:SER33 4.7 113.8 1.0
F2 A:JT3301 4.7 69.0 1.0
O5 A:JT3301 4.8 61.5 1.0
C A:HIS257 4.8 79.8 1.0
CA A:HIS257 4.9 75.9 1.0

Fluorine binding site 5 out of 5 in 7zsp

Go back to Fluorine Binding Sites List in 7zsp
Fluorine binding site 5 out of 5 in the Human Purine Nucleoside Phosphorylase in Complex with Js-555


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Purine Nucleoside Phosphorylase in Complex with Js-555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:76.2
occ:1.00
 F5 A:JT3301 0.0 76.2 1.0
C16 A:JT3301 1.3 73.8 1.0
C17 A:JT3301 2.4 74.9 1.0
C15 A:JT3301 2.4 70.1 1.0
F4 A:JT3301 2.7 86.3 1.0
O5 A:JT3301 2.8 61.5 1.0
C10 A:JT3301 3.1 57.0 1.0
C9 A:JT3301 3.2 55.9 1.0
OG A:SER33 3.5 113.8 1.0
CG1 A:VAL260 3.6 66.3 1.0
C18 A:JT3301 3.6 70.8 1.0
C20 A:JT3301 3.6 69.4 1.0
O A:HIS257 3.6 89.1 1.0
CB A:VAL260 3.8 68.9 1.0
CB A:HIS257 3.8 78.7 1.0
C19 A:JT3301 4.1 71.1 1.0
CG A:LEU261 4.2 93.7 1.0
C11 A:JT3301 4.2 63.1 1.0
CA A:HIS257 4.2 75.9 1.0
CD2 A:LEU261 4.3 94.0 1.0
C8 A:JT3301 4.3 57.1 1.0
C A:HIS257 4.4 79.8 1.0
CB A:SER33 4.4 108.7 1.0
N A:LEU261 4.5 80.4 1.0
ND1 A:HIS257 4.5 94.0 1.0
CG2 A:VAL260 4.6 68.4 1.0
CG A:HIS257 4.6 89.8 1.0
F3 A:JT3301 4.7 81.4 1.0
F1 A:JT3301 4.7 70.6 1.0
C A:VAL260 4.9 72.7 1.0
CA A:VAL260 4.9 74.0 1.0

Reference:

J.Skacel, S.Djukic. Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Pnp Inhibitors To Be Published.
Page generated: Fri Aug 2 16:19:23 2024

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