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Fluorine in PDB 6woi: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds, PDB code: 6woi was solved by G.N.Zong, H.C.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.63 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.503, 59.608, 62.353, 90, 90, 90
R / Rfree (%) 14.5 / 16.7

Other elements in 6woi:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds 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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds (pdb code 6woi). 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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds, PDB code: 6woi:

Fluorine binding site 1 out of 1 in 6woi

Go back to Fluorine Binding Sites List in 6woi
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds


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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:44.3
occ:1.00
 MG A:MG404 2.0 35.7 1.0
MG A:MG403 2.1 31.7 1.0
O A:HOH538 2.2 34.6 1.0
O A:HOH513 2.4 59.9 1.0
O A:HOH525 2.5 34.5 1.0
O47 A:O81401 3.1 21.1 1.0
O A:HOH510 3.1 32.3 1.0
P7 A:O81401 3.2 19.8 1.0
O37 A:O81401 3.2 20.3 1.0
O27 A:O81401 3.3 18.7 1.0
OE2 A:GLU69 3.3 24.9 1.0
OE1 A:GLU66 3.5 17.6 1.0
OE2 A:GLU66 3.5 15.0 1.0
O A:HOH558 3.8 37.6 1.0
CD A:GLU66 3.9 14.1 1.0
O A:HOH509 4.3 27.9 1.0
CD A:GLU69 4.5 20.3 1.0
OE1 A:GLU70 4.5 13.8 1.0
O41 A:O81401 4.8 19.7 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 17:12:47 2025

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