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

Magnesium in PDB 6woc: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride., PDB code: 6woc 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) 31.40 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.708, 59.611, 62.581, 90, 90, 90
R / Rfree (%) 13.8 / 16.4

Other elements in 6woc:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. (pdb code 6woc). 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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride., PDB code: 6woc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.


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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.8
occ:1.00
 O35 A:I7P401 2.0 11.8 1.0
O44 A:I7P401 2.1 13.6 1.0
OE1 A:GLU70 2.1 12.4 1.0
O A:HOH523 2.1 10.9 1.0
O55 A:I7P401 2.1 13.9 1.0
O A:GLY50 2.1 11.1 1.0
CD A:GLU70 3.0 11.4 1.0
PA5 A:I7P401 3.2 13.0 1.0
PA4 A:I7P401 3.2 13.7 1.0
MG A:MG403 3.3 33.3 1.0
C A:GLY50 3.3 10.0 1.0
PB5 A:I7P401 3.3 18.9 1.0
OE2 A:GLU70 3.4 11.7 1.0
O45 A:I7P401 3.5 15.8 1.0
O14 A:I7P401 3.6 15.8 1.0
O24 A:I7P401 3.7 15.8 1.0
CA A:GLY51 3.7 10.3 1.0
O A:HOH614 3.8 43.1 1.0
O15 A:I7P401 3.9 15.7 1.0
N A:GLY51 4.0 9.8 1.0
OE2 A:GLU66 4.1 16.8 1.0
O75 A:I7P401 4.1 22.4 1.0
NH2 A:ARG20 4.2 15.3 1.0
CG A:GLU70 4.4 11.7 1.0
O A:HOH539 4.4 16.3 1.0
O25 A:I7P401 4.5 12.4 1.0
N A:GLY50 4.5 9.9 1.0
O34 A:I7P401 4.5 17.3 1.0
CA A:GLY50 4.5 10.1 1.0
O65 A:I7P401 4.5 21.3 1.0
NH2 A:ARG115 4.6 18.5 1.0
C5 A:I7P401 4.7 17.0 1.0
C4 A:I7P401 4.7 16.4 1.0

Magnesium binding site 2 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.


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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:33.3
occ:1.00
 O55 A:I7P401 2.1 13.9 1.0
O A:HOH509 2.1 28.1 1.0
O A:HOH625 2.3 38.8 1.0
OE1 A:GLU70 2.3 12.4 1.0
O A:HOH614 2.4 43.1 1.0
OE2 A:GLU66 2.4 16.8 1.0
PB5 A:I7P401 3.2 18.9 1.0
CD A:GLU70 3.2 11.4 1.0
MG A:MG402 3.3 10.8 1.0
CD A:GLU66 3.4 14.9 1.0
CG A:GLU70 3.4 11.7 1.0
MG A:MG404 3.7 30.1 1.0
O75 A:I7P401 3.7 22.4 1.0
O65 A:I7P401 3.8 21.3 1.0
OE1 A:GLU66 3.8 18.2 1.0
O44 A:I7P401 3.8 13.6 1.0
OE2 A:GLU69 3.9 26.2 1.0
O A:HOH551 4.0 30.0 1.0
O A:GLY50 4.1 11.1 1.0
O A:HOH550 4.2 34.1 1.0
OE2 A:GLU70 4.4 11.7 1.0
O45 A:I7P401 4.5 15.8 1.0
OD2 A:ASP109 4.7 17.0 1.0
CA A:GLY51 4.7 10.3 1.0
CG A:GLU66 4.7 13.8 1.0
NH2 A:ARG115 4.8 18.5 1.0
C A:GLY50 4.8 10.0 1.0
O35 A:I7P401 4.8 11.8 1.0
CB A:GLU70 4.9 11.7 1.0
O A:HOH523 5.0 10.9 1.0
CB A:GLU69 5.0 15.9 1.0

Magnesium binding site 3 out of 3 in 6woc

Go back to Magnesium Binding Sites List in 6woc
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.


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 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.1
occ:1.00
 O A:HOH550 1.9 34.1 1.0
O A:HOH548 2.0 22.2 1.0
O65 A:I7P401 2.0 21.3 1.0
O A:HOH625 2.3 38.8 1.0
OE1 A:GLU66 2.3 18.2 1.0
O A:HOH631 2.5 38.4 1.0
PB5 A:I7P401 3.1 18.9 1.0
CD A:GLU66 3.3 14.9 1.0
OE2 A:GLU66 3.6 16.8 1.0
MG A:MG403 3.7 33.3 1.0
O55 A:I7P401 3.7 13.9 1.0
O A:HOH521 3.7 38.3 1.0
O75 A:I7P401 3.8 22.4 1.0
NH1 A:ARG65 3.9 15.1 1.0
OE2 A:GLU69 4.0 26.2 1.0
N A:GLY52 4.1 10.9 1.0
O A:HOH562 4.1 31.8 1.0
O A:GLY52 4.2 13.8 1.0
O45 A:I7P401 4.4 15.8 1.0
O A:HOH509 4.5 28.1 1.0
CG A:GLU66 4.6 13.8 1.0
CA A:GLY51 4.8 10.3 1.0
CA A:GLY52 4.8 10.7 1.0
C A:GLY51 4.8 9.5 1.0
NH2 A:ARG65 4.8 14.5 1.0
CZ A:ARG65 4.8 13.9 1.0
C A:GLY52 5.0 11.1 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 23:05:08 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy