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Magnesium in PDB 6woa: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion, PDB code: 6woa 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) 37.71 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.496, 59.717, 61.887, 90, 90, 90
R / Rfree (%) 12.9 / 14.8

Other elements in 6woa:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion (pdb code 6woa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion, PDB code: 6woa:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6woa

Go back to Magnesium Binding Sites List in 6woa
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:7.5
occ:1.00
 O46 A:UEV401 2.1 25.6 1.0
O A:GLY50 2.2 9.3 1.0
OE1 A:GLU70 2.3 13.7 1.0
O25 A:UEV401 2.3 12.7 1.0
O65 A:UEV401 2.4 17.8 1.0
O A:HOH595 2.6 15.2 1.0
OE2 A:GLU70 2.8 10.0 1.0
CD A:GLU70 2.9 11.1 1.0
C A:GLY50 3.4 9.1 1.0
PA6 A:UEV401 3.5 21.5 1.0
PA5 A:UEV401 3.6 14.4 1.0
O16 A:UEV401 3.7 21.7 1.0
MG A:MG403 3.7 22.8 1.0
PB5 A:UEV401 3.8 16.4 1.0
O45 A:UEV401 3.9 16.1 1.0
CA A:GLY51 4.1 8.9 1.0
O A:HOH548 4.2 26.1 1.0
N A:GLY50 4.2 9.5 1.0
N A:GLY51 4.2 9.0 1.0
NH1 A:ARG20 4.2 11.3 1.0
O36 A:UEV401 4.3 23.9 1.0
O15 A:UEV401 4.4 17.4 1.0
CG A:GLU70 4.4 11.3 1.0
CA A:GLY50 4.4 9.2 1.0
NH2 A:ARG115 4.5 20.6 1.0
O A:HOH502 4.5 17.8 1.0
OE2 A:GLU66 4.5 17.8 1.0
CD1 A:ILE47 4.7 12.3 1.0
O26 A:UEV401 4.7 21.2 1.0
O55 A:UEV401 4.7 16.8 1.0
O A:HOH503 4.7 44.9 1.0
O75 A:UEV401 4.7 19.2 1.0
C5 A:UEV401 4.8 20.9 1.0
O35 A:UEV401 4.9 15.2 1.0
NH1 A:ARG115 4.9 16.0 1.0
C6 A:UEV401 4.9 22.4 1.0
CZ A:ARG115 5.0 19.8 1.0

Magnesium binding site 2 out of 3 in 6woa

Go back to Magnesium Binding Sites List in 6woa
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:22.8
occ:1.00
 F A:F407 1.8 26.6 1.0
O A:HOH548 2.0 26.1 1.0
O A:HOH554 2.0 33.9 1.0
OE1 A:GLU70 2.2 13.7 1.0
O65 A:UEV401 2.3 17.8 1.0
OE2 A:GLU66 2.4 17.8 1.0
CD A:GLU70 3.2 11.1 1.0
MG A:MG404 3.3 24.4 1.0
PB5 A:UEV401 3.3 16.4 1.0
CD A:GLU66 3.4 17.0 1.0
CG A:GLU70 3.6 11.3 1.0
O75 A:UEV401 3.6 19.2 1.0
OE1 A:GLU66 3.7 18.9 1.0
MG A:MG402 3.7 7.5 1.0
O55 A:UEV401 3.7 16.8 1.0
O A:HOH633 4.0 53.1 1.0
O A:HOH503 4.0 44.9 1.0
O A:GLY50 4.0 9.3 1.0
OE2 A:GLU69 4.0 24.1 1.0
O A:HOH558 4.1 28.1 1.0
O A:HOH507 4.2 33.6 1.0
OE2 A:GLU70 4.3 10.0 1.0
NH2 A:ARG115 4.6 20.6 1.0
CA A:GLY51 4.7 8.9 1.0
O A:HOH611 4.7 36.8 1.0
O46 A:UEV401 4.7 25.6 1.0
CG A:GLU66 4.7 14.6 1.0
O45 A:UEV401 4.8 16.1 1.0
OD2 A:ASP109 4.8 17.1 1.0
C A:GLY50 4.8 9.1 1.0

Magnesium binding site 3 out of 3 in 6woa

Go back to Magnesium Binding Sites List in 6woa
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 2-Diphosphoinositol Pentakisphosphate (2-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:24.4
occ:1.00
 F A:F407 1.9 26.6 1.0
O A:HOH558 2.2 28.1 1.0
O A:HOH542 2.2 21.8 1.0
O A:HOH611 2.2 36.8 1.0
O75 A:UEV401 2.3 19.2 1.0
OE1 A:GLU66 2.3 18.9 1.0
CD A:GLU66 3.2 17.0 1.0
MG A:MG403 3.3 22.8 1.0
PB5 A:UEV401 3.4 16.4 1.0
OE2 A:GLU66 3.5 17.8 1.0
O55 A:UEV401 3.7 16.8 1.0
O65 A:UEV401 3.8 17.8 1.0
N A:GLY52 4.0 9.8 1.0
O A:HOH633 4.0 53.1 1.0
O A:HOH618 4.1 50.4 1.0
O A:HOH545 4.2 25.5 1.0
NH1 A:ARG65 4.2 15.3 1.0
OE2 A:GLU69 4.2 24.1 1.0
O A:HOH554 4.3 33.9 1.0
O A:GLY52 4.3 11.6 1.0
O A:HOH548 4.5 26.1 1.0
CG A:GLU66 4.6 14.6 1.0
CA A:GLY51 4.7 8.9 1.0
C A:GLY51 4.7 9.8 1.0
CA A:GLY52 4.8 10.0 1.0
O45 A:UEV401 4.8 16.1 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 Oct 1 23:03:51 2024

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