Fluorine in PDB 7tn4: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4 was solved by G.Zong, H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.40 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.149, 59.743, 62.769, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 7tn4:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion (pdb code 7tn4). 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4:

Fluorine binding site 1 out of 1 in 7tn4

Go back to Fluorine Binding Sites List in 7tn4
Fluorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:19.6
occ:1.00
 MG A:MG503 1.8 18.7 1.0
MG A:MG502 2.1 16.6 1.0
O A:HOH602 2.3 16.9 1.0
O63 A:ZM2507 2.6 21.2 1.0
PB3 A:ZM2507 2.7 29.3 1.0
O A:HOH629 2.7 19.6 1.0
O53 A:ZM2507 2.8 15.3 1.0
O A:HOH663 2.9 18.5 1.0
O A:HOH690 2.9 17.4 1.0
OE1 A:GLU66 3.0 13.8 1.0
O A:HOH672 3.0 13.6 1.0
OE2 A:GLU66 3.0 12.5 1.0
O73 A:ZM2507 3.2 22.6 1.0
O A:HOH730 3.3 32.6 1.0
CD A:GLU66 3.4 14.0 1.0
OE2 A:GLU69 3.8 20.9 1.0
O A:HOH660 3.9 23.4 1.0
O A:HOH718 3.9 33.3 1.0
OE1 A:GLU70 4.2 15.1 1.0
O23 A:ZM2507 4.4 22.3 1.0
O A:HOH638 4.5 24.0 1.0
MG A:MG501 4.7 13.8 1.0
O42 A:ZM2507 4.8 16.8 1.0
CG A:GLU66 4.9 12.9 1.0
CA A:GLY51 4.9 13.4 1.0

Reference:

G.Zong, S.B.Shears, H.Wang. Structural and Catalytic Analyses of the Insp 6 Kinase Activities of Higher Plant Itpks. Faseb J. V. 36 22380 2022.
ISSN: ESSN 1530-6860
PubMed: 35635723
DOI: 10.1096/FJ.202200393R
Page generated: Wed Apr 5 01:15:54 2023

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