Atomistry » Magnesium » PDB 6whm-6wpf » 6woi
Atomistry »
  Magnesium »
    PDB 6whm-6wpf »
      6woi »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy