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Magnesium in PDB 6wob: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion, PDB code: 6wob was solved by G.N.Zong, H.C.Wang, B.S.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.01 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.607, 59.541, 62.47, 90, 90, 90
R / Rfree (%) 16 / 20.3

Other elements in 6wob:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion 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 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion (pdb code 6wob). 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 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion, PDB code: 6wob:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wob

Go back to Magnesium Binding Sites List in 6wob
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-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 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.7
occ:1.00
 O35 A:U71401 2.0 11.4 1.0
O34 A:U71401 2.0 13.6 1.0
O54 A:U71401 2.0 11.4 1.0
OE1 A:GLU70 2.1 18.4 1.0
O A:GLY50 2.1 16.7 1.0
O A:HOH522 2.1 13.7 1.0
CD A:GLU70 3.0 13.5 1.0
PA5 A:U71401 3.2 10.2 1.0
PA4 A:U71401 3.2 9.6 1.0
MG A:MG403 3.3 16.8 1.0
C A:GLY50 3.3 15.0 1.0
OE2 A:GLU70 3.3 12.3 1.0
PB4 A:U71401 3.3 10.1 1.0
O15 A:U71401 3.5 11.0 1.0
O44 A:U71401 3.5 9.6 1.0
O A:HOH565 3.7 20.7 1.0
CA A:GLY51 3.7 11.5 1.0
O45 A:U71401 3.8 11.6 1.0
O14 A:U71401 3.9 9.6 1.0
N A:GLY51 4.0 11.3 1.0
OE2 A:GLU66 4.0 14.2 1.0
O74 A:U71401 4.1 11.0 1.0
NH1 A:ARG20 4.1 14.3 1.0
CG A:GLU70 4.4 12.4 1.0
O A:HOH534 4.4 21.1 1.0
N A:GLY50 4.5 13.4 1.0
O24 A:U71401 4.5 11.4 1.0
O64 A:U71401 4.5 11.7 1.0
CA A:GLY50 4.5 14.2 1.0
O25 A:U71401 4.5 11.7 1.0
NH2 A:ARG115 4.5 15.5 1.0
C5 A:U71401 4.6 10.8 1.0
F A:F407 4.7 20.4 1.0
C4 A:U71401 4.7 10.3 1.0
CD A:GLU66 4.9 13.2 1.0
O A:HOH533 5.0 18.5 1.0
O A:HOH549 5.0 24.4 1.0

Magnesium binding site 2 out of 3 in 6wob

Go back to Magnesium Binding Sites List in 6wob
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-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 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:16.8
occ:1.00
 F A:F407 1.9 20.4 1.0
O A:HOH533 2.0 18.5 1.0
O54 A:U71401 2.1 11.4 1.0
OE2 A:GLU66 2.2 14.2 1.0
OE1 A:GLU70 2.2 18.4 1.0
O A:HOH565 2.3 20.7 1.0
PB4 A:U71401 3.1 10.1 1.0
CD A:GLU66 3.2 13.2 1.0
CD A:GLU70 3.2 13.5 1.0
MG A:MG402 3.3 21.7 1.0
MG A:MG404 3.5 19.6 1.0
CG A:GLU70 3.5 12.4 1.0
OE1 A:GLU66 3.5 15.2 1.0
O A:HOH504 3.6 28.6 1.0
O64 A:U71401 3.6 11.7 1.0
O74 A:U71401 3.6 11.0 1.0
O35 A:U71401 3.8 11.4 1.0
OE2 A:GLU69 3.9 17.9 1.0
O A:GLY50 4.0 16.7 1.0
O A:HOH622 4.1 32.3 1.0
O A:HOH524 4.3 22.2 1.0
O A:HOH512 4.4 24.1 1.0
OE2 A:GLU70 4.4 12.3 1.0
O A:HOH595 4.5 26.4 1.0
O44 A:U71401 4.5 9.6 1.0
CA A:GLY51 4.5 11.5 1.0
CG A:GLU66 4.6 13.1 1.0
C A:GLY50 4.7 15.0 1.0
O34 A:U71401 4.8 13.6 1.0
NH2 A:ARG115 4.8 15.5 1.0
CB A:GLU66 4.9 12.9 1.0
O A:HOH600 4.9 28.2 1.0
O A:HOH522 5.0 13.7 1.0
CB A:GLU70 5.0 11.8 1.0

Magnesium binding site 3 out of 3 in 6wob

Go back to Magnesium Binding Sites List in 6wob
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 4-Diphosphoinositol Pentakisphosphate (4-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 4-Diphosphoinositol Pentakisphosphate (4-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:19.6
occ:1.00
 F A:F407 2.0 20.4 1.0
O A:HOH524 2.1 22.2 1.0
O64 A:U71401 2.1 11.7 1.0
O A:HOH521 2.1 15.9 1.0
OE1 A:GLU66 2.2 15.2 1.0
O A:HOH600 2.2 28.2 1.0
PB4 A:U71401 3.2 10.1 1.0
CD A:GLU66 3.2 13.2 1.0
MG A:MG403 3.5 16.8 1.0
OE2 A:GLU66 3.6 14.2 1.0
O54 A:U71401 3.7 11.4 1.0
O74 A:U71401 3.8 11.0 1.0
O A:HOH504 3.8 28.6 1.0
NH1 A:ARG65 3.9 13.5 1.0
OE2 A:GLU69 4.0 17.9 1.0
O A:HOH620 4.0 40.9 1.0
N A:GLY52 4.1 11.4 1.0
O A:HOH502 4.2 36.2 1.0
O A:HOH569 4.2 22.9 1.0
O A:GLY52 4.2 12.5 1.0
O A:HOH533 4.3 18.5 1.0
O A:HOH622 4.4 32.3 1.0
O44 A:U71401 4.5 9.6 1.0
CG A:GLU66 4.6 13.1 1.0
CA A:GLY52 4.8 11.5 1.0
O A:HOH565 4.8 20.7 1.0
CA A:GLY51 4.8 11.5 1.0
C A:GLY51 4.8 11.1 1.0
CZ A:ARG65 4.9 12.9 1.0
NH2 A:ARG65 4.9 13.0 1.0
C A:GLY52 5.0 12.3 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 23:04:10 2024

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