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Magnesium 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
Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where 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:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6woi

Go back to Magnesium Binding Sites List in 6woi
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg402

b:16.2
occ:1.00
 O A:HOH562 1.9 15.5 1.0
O27 A:O81401 2.0 18.7 1.0
O21 A:O81401 2.1 15.5 1.0
OE1 A:GLU70 2.2 13.8 1.0
O A:GLY50 2.2 8.5 1.0
O36 A:O81401 2.2 25.4 1.0
CD A:GLU70 3.1 13.1 1.0
P1 A:O81401 3.3 15.8 1.0
P7 A:O81401 3.4 19.8 1.0
MG A:MG403 3.4 31.7 1.0
C A:GLY50 3.4 8.6 1.0
OE2 A:GLU70 3.4 12.4 1.0
P6 A:O81401 3.4 22.3 1.0
O41 A:O81401 3.5 19.7 1.0
O16 A:O81401 3.7 19.2 1.0
CA A:GLY51 3.7 10.0 1.0
O A:HOH510 3.7 32.3 1.0
O46 A:O81401 3.9 23.3 1.0
O11 A:O81401 4.0 23.0 1.0
N A:GLY51 4.0 9.6 1.0
OE2 A:GLU66 4.1 15.0 1.0
O A:HOH514 4.2 23.1 1.0
O47 A:O81401 4.2 21.1 1.0
NH1 A:ARG20 4.3 11.7 1.0
CG A:GLU70 4.4 12.9 1.0
O31 A:O81401 4.5 14.6 1.0
N A:GLY50 4.5 9.2 1.0
O37 A:O81401 4.5 20.3 1.0
CA A:GLY50 4.6 8.9 1.0
NH2 A:ARG115 4.6 19.5 1.0
C1 A:O81401 4.7 21.4 1.0
O26 A:O81401 4.8 24.9 1.0
C6 A:O81401 4.8 19.2 1.0
O A:HOH525 5.0 34.5 1.0

Magnesium binding site 2 out of 3 in 6woi

Go back to Magnesium Binding Sites List in 6woi
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg403

b:31.7
occ:1.00
 O A:HOH525 1.9 34.5 1.0
F A:F407 2.1 44.3 1.0
O27 A:O81401 2.1 18.7 1.0
OE2 A:GLU66 2.2 15.0 1.0
OE1 A:GLU70 2.5 13.8 1.0
O A:HOH510 2.5 32.3 1.0
P7 A:O81401 3.1 19.8 1.0
CD A:GLU66 3.2 14.1 1.0
MG A:MG404 3.3 35.7 1.0
MG A:MG402 3.4 16.2 1.0
CD A:GLU70 3.4 13.1 1.0
OE1 A:GLU66 3.5 17.6 1.0
O47 A:O81401 3.6 21.1 1.0
O37 A:O81401 3.6 20.3 1.0
CG A:GLU70 3.6 12.9 1.0
OE2 A:GLU69 3.8 24.9 1.0
O A:HOH538 3.9 34.6 1.0
O36 A:O81401 3.9 25.4 1.0
O A:GLY50 4.1 8.5 1.0
O A:HOH513 4.2 59.9 1.0
O A:HOH558 4.3 37.6 1.0
O41 A:O81401 4.5 19.7 1.0
CA A:GLY51 4.5 10.0 1.0
OE2 A:GLU70 4.6 12.4 1.0
CG A:GLU66 4.6 14.2 1.0
C A:GLY50 4.8 8.6 1.0
NH2 A:ARG115 4.9 19.5 1.0
OD2 A:ASP109 4.9 18.5 1.0
O21 A:O81401 5.0 15.5 1.0
CB A:GLU66 5.0 13.6 1.0
CD A:GLU69 5.0 20.3 1.0
O A:HOH562 5.0 15.5 1.0

Magnesium binding site 3 out of 3 in 6woi

Go back to Magnesium Binding Sites List in 6woi
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg404

b:35.7
occ:1.00
 O A:HOH538 1.9 34.6 1.0
F A:F407 2.0 44.3 1.0
O37 A:O81401 2.2 20.3 1.0
O A:HOH509 2.3 27.9 1.0
OE1 A:GLU66 2.4 17.6 1.0
O A:HOH513 2.7 59.9 1.0
P7 A:O81401 3.2 19.8 1.0
MG A:MG403 3.3 31.7 1.0
CD A:GLU66 3.3 14.1 1.0
O47 A:O81401 3.6 21.1 1.0
OE2 A:GLU66 3.6 15.0 1.0
O27 A:O81401 3.7 18.7 1.0
OE2 A:GLU69 4.0 24.9 1.0
NH1 A:ARG65 4.0 15.8 1.0
O A:HOH567 4.1 33.9 1.0
O A:HOH525 4.1 34.5 1.0
N A:GLY52 4.1 10.6 1.0
O A:GLY52 4.3 13.9 1.0
O41 A:O81401 4.5 19.7 1.0
CG A:GLU66 4.7 14.2 1.0
CA A:GLY51 4.8 10.0 1.0
O A:HOH510 4.8 32.3 1.0
C A:GLY51 4.8 9.6 1.0
CA A:GLY52 4.9 10.8 1.0
CZ A:ARG65 4.9 14.2 1.0
NH2 A:ARG65 4.9 15.1 1.0
CD A:GLU69 5.0 20.3 1.0
O A:HOH591 5.0 41.4 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 Oct 1 23:05:50 2024

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