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Fluorine in PDB 6wob: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion, PDB code: 6wob was solved by G.N.Zong, H.C.Wang, B.S.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.01 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.607, 59.541, 62.47, 90, 90, 90
R / Rfree (%) 16 / 20.3

Other elements in 6wob:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion (pdb code 6wob). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion, PDB code: 6wob:

Fluorine binding site 1 out of 1 in 6wob

Go back to Fluorine Binding Sites List in 6wob
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:20.4
occ:1.00
 MG A:MG403 1.9 16.8 1.0
MG A:MG404 2.0 19.6 1.0
O A:HOH504 2.5 28.6 1.0
O A:HOH533 2.7 18.5 1.0
O A:HOH524 2.7 22.2 1.0
O64 A:U71401 2.8 11.7 1.0
O54 A:U71401 2.8 11.4 1.0
PB4 A:U71401 2.8 10.1 1.0
O A:HOH565 2.9 20.7 1.0
O A:HOH622 3.0 32.3 1.0
O74 A:U71401 3.1 11.0 1.0
O A:HOH600 3.1 28.2 1.0
OE1 A:GLU66 3.1 15.2 1.0
OE2 A:GLU66 3.1 14.2 1.0
OE2 A:GLU69 3.5 17.9 1.0
CD A:GLU66 3.5 13.2 1.0
O A:HOH620 3.8 40.9 1.0
O A:HOH521 4.1 15.9 1.0
OE1 A:GLU70 4.1 18.4 1.0
O A:HOH512 4.3 24.1 1.0
O44 A:U71401 4.5 9.6 1.0
MG A:MG402 4.7 21.7 1.0
CD A:GLU69 4.8 15.4 1.0
O A:HOH595 4.9 26.4 1.0
O35 A:U71401 4.9 11.4 1.0

Reference:

G.Zong, N.Jork, S.Hostachy, D.Fiedler, H.J.Jessen, S.B.Shears, H.Wang. New Structural Insights Reveal An Expanded Reaction Cycle For Inositol Pyrophosphate Hydrolysis By Human DIPP1. Faseb J. V. 35 21275 2021.
ISSN: ESSN 1530-6860
PubMed: 33475202
DOI: 10.1096/FJ.202001489R
Page generated: Tue Jul 15 17:12:43 2025

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