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Magnesium in PDB 8g9c: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7, PDB code: 8g9c was solved by G.Zong, H.Wang, S.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.72 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.752, 59.639, 62.409, 90, 90, 90
R / Rfree (%) 17 / 18.8

Other elements in 8g9c:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 (pdb code 8g9c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7, PDB code: 8g9c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8g9c

Go back to Magnesium Binding Sites List in 8g9c
Magnesium binding site 1 out of 4 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7


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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.4
occ:1.00
 O A:HOH558 1.9 23.3 1.0
O A:HOH517 1.9 24.8 1.0
O A:GLY50 2.1 14.1 1.0
OE1 A:GLU70 2.2 19.2 1.0
O22 A:YUT401 2.2 18.5 1.0
O23 A:YUT401 2.7 33.5 1.0
CD A:GLU70 3.1 17.1 1.0
C A:GLY50 3.3 12.9 1.0
MG A:MG403 3.3 28.4 1.0
PA2 A:YUT401 3.3 17.8 1.0
O32 A:YUT401 3.4 22.2 1.0
OE2 A:GLU70 3.4 16.5 1.0
CA A:GLY51 3.6 12.9 1.0
MG A:MG405 3.6 41.0 1.0
O A:HOH569 3.8 31.7 1.0
PA3 A:YUT401 3.9 32.2 1.0
O A:HOH509 3.9 43.6 1.0
N A:GLY51 3.9 11.8 1.0
O13 A:YUT401 4.0 25.7 1.0
O12 A:YUT401 4.1 20.8 1.0
OE2 A:GLU66 4.1 20.3 1.0
NH1 A:ARG20 4.1 13.2 1.0
O33 A:YUT401 4.2 30.5 1.0
CG A:GLU70 4.5 16.8 1.0
F A:F408 4.5 34.1 1.0
N A:GLY50 4.5 12.3 1.0
CA A:GLY50 4.5 12.4 1.0
O A:HOH535 4.5 26.2 1.0
C2 A:YUT401 4.6 20.4 1.0
O42 A:YUT401 4.6 18.4 1.0
NH2 A:ARG115 4.7 21.4 1.0
O A:HOH512 4.9 25.2 1.0
C3 A:YUT401 5.0 21.1 1.0
CD A:GLU66 5.0 19.1 1.0
C A:GLY51 5.0 12.6 1.0

Magnesium binding site 2 out of 4 in 8g9c

Go back to Magnesium Binding Sites List in 8g9c
Magnesium binding site 2 out of 4 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7


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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:28.4
occ:1.00
 O A:HOH521 2.0 32.1 1.0
O A:HOH517 2.0 24.8 1.0
F A:F408 2.0 34.1 1.0
O A:HOH569 2.2 31.7 1.0
OE2 A:GLU66 2.3 20.3 1.0
OE1 A:GLU70 2.3 19.2 1.0
CD A:GLU66 3.3 19.1 1.0
MG A:MG402 3.3 21.4 1.0
CD A:GLU70 3.3 17.1 1.0
MG A:MG405 3.3 41.0 1.0
MG A:MG404 3.4 32.4 1.0
CG A:GLU70 3.5 16.8 1.0
OE1 A:GLU66 3.6 20.6 1.0
O A:HOH509 3.7 43.6 1.0
OE2 A:GLU69 4.0 29.7 1.0
O A:GLY50 4.0 14.1 1.0
O A:HOH513 4.1 31.5 1.0
O A:HOH515 4.1 40.9 1.0
O A:HOH512 4.1 25.2 1.0
O23 A:YUT401 4.2 33.5 1.0
OE2 A:GLU70 4.4 16.5 1.0
CA A:GLY51 4.5 12.9 1.0
CG A:GLU66 4.6 17.5 1.0
NH2 A:ARG115 4.8 21.4 1.0
C A:GLY50 4.8 12.9 1.0
O A:HOH604 4.8 39.4 1.0
O A:HOH558 4.8 23.3 1.0
OD2 A:ASP109 4.8 20.7 1.0
O32 A:YUT401 4.8 22.2 1.0
CB A:GLU66 5.0 16.2 1.0

Magnesium binding site 3 out of 4 in 8g9c

Go back to Magnesium Binding Sites List in 8g9c
Magnesium binding site 3 out of 4 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7


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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:32.4
occ:1.00
 F A:F408 1.8 34.1 1.0
O A:HOH513 2.1 31.5 1.0
O A:HOH604 2.1 39.4 1.0
OE1 A:GLU66 2.2 20.6 1.0
O A:HOH542 2.2 31.1 1.0
O A:HOH512 2.2 25.2 1.0
MG A:MG405 3.2 41.0 1.0
CD A:GLU66 3.2 19.1 1.0
MG A:MG403 3.4 28.4 1.0
OE2 A:GLU66 3.5 20.3 1.0
O A:HOH517 3.7 24.8 1.0
NH1 A:ARG65 3.9 18.4 1.0
O A:HOH507 3.9 47.0 1.0
OE2 A:GLU69 4.0 29.7 1.0
O A:HOH521 4.0 32.1 1.0
N A:GLY52 4.1 14.4 1.0
O A:GLY52 4.3 16.6 1.0
O A:HOH549 4.4 43.0 1.0
CG A:GLU66 4.6 17.5 1.0
O A:HOH509 4.6 43.6 1.0
O A:HOH591 4.6 51.2 1.0
CA A:GLY51 4.8 12.9 1.0
O A:HOH569 4.8 31.7 1.0
NH2 A:ARG65 4.8 18.0 1.0
CZ A:ARG65 4.8 17.7 1.0
C A:GLY51 4.8 12.6 1.0
CA A:GLY52 4.9 14.4 1.0

Magnesium binding site 4 out of 4 in 8g9c

Go back to Magnesium Binding Sites List in 8g9c
Magnesium binding site 4 out of 4 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:41.0
occ:1.00
 O A:HOH512 2.0 25.2 1.0
O A:HOH517 2.1 24.8 1.0
O A:HOH509 2.1 43.6 1.0
O32 A:YUT401 2.2 22.2 1.0
O A:HOH507 2.2 47.0 1.0
F A:F408 2.5 34.1 1.0
MG A:MG404 3.2 32.4 1.0
MG A:MG403 3.3 28.4 1.0
O31 A:YUT401 3.6 31.0 1.0
PA2 A:YUT401 3.6 17.8 1.0
O A:HOH549 3.6 43.0 1.0
MG A:MG402 3.6 21.4 1.0
O A:HOH604 3.7 39.4 1.0
O23 A:YUT401 3.8 33.5 1.0
O A:HOH569 3.9 31.7 1.0
N A:GLY52 4.0 14.4 1.0
O22 A:YUT401 4.0 18.5 1.0
CA A:GLY51 4.1 12.9 1.0
OE1 A:GLU66 4.3 20.6 1.0
NZ A:LYS18 4.4 20.0 0.5
OE2 A:GLU66 4.5 20.3 1.0
O42 A:YUT401 4.5 18.4 1.0
C2 A:YUT401 4.6 20.4 1.0
OE1 A:GLU70 4.6 19.2 1.0
O12 A:YUT401 4.6 20.8 1.0
C A:GLY51 4.6 12.6 1.0
O A:HOH542 4.7 31.1 1.0
CD A:GLU66 4.8 19.1 1.0
PA1 A:YUT401 4.8 28.6 1.0
O A:GLY50 4.9 14.1 1.0
O A:HOH513 4.9 31.5 1.0
O11 A:YUT401 4.9 24.6 1.0
O A:HOH521 5.0 32.1 1.0

Reference:

S.Hostachy, H.Wang, G.Zong, K.Franke, A.M.Riley, P.Schmieder, B.V.L.Potter, S.B.Shears, D.Fiedler. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry V. 29 02426 2023.
ISSN: ISSN 0947-6539
PubMed: 37773020
DOI: 10.1002/CHEM.202302426
Page generated: Fri Aug 15 05:09:59 2025

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