Atomistry » Fluorine » PDB 8fv2-8g9d » 8g9c
Atomistry »
  Fluorine »
    PDB 8fv2-8g9d »
      8g9c »

Fluorine 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
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F401

b:41.4
occ:1.00
 F51 A:YUT401 0.0 41.4 1.0
C45 A:YUT401 1.3 51.5 1.0
F52 A:YUT401 2.2 56.8 1.0
PA5 A:YUT401 2.6 58.0 1.0
PB5 A:YUT401 2.6 51.3 1.0
O15 A:YUT401 2.7 37.7 1.0
O36 A:YUT401 2.8 33.7 1.0
O65 A:YUT401 3.0 42.7 1.0
O A:HOH504 3.0 32.6 1.0
O75 A:YUT401 3.0 58.1 1.0
NE A:ARG89 3.3 33.6 1.0
O25 A:YUT401 3.5 56.5 1.0
CD A:ARG89 3.7 28.5 1.0
O35 A:YUT401 3.8 62.0 1.0
CZ A:ARG89 3.9 40.5 1.0
O55 A:YUT401 3.9 52.9 1.0
CG A:ARG89 3.9 26.8 1.0
C5 A:YUT401 4.1 27.2 1.0
NH2 A:ARG89 4.1 40.5 1.0
PA6 A:YUT401 4.2 32.5 1.0
O16 A:YUT401 4.6 29.4 1.0
C6 A:YUT401 4.7 26.0 1.0
O A:HOH590 4.7 38.0 1.0
NH1 A:ARG89 4.7 42.0 1.0
O26 A:YUT401 4.8 39.5 1.0
C4 A:YUT401 4.8 22.0 1.0
CB A:ARG89 4.9 21.6 1.0
O14 A:YUT401 4.9 25.3 1.0

Fluorine binding site 2 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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:F401

b:56.8
occ:1.00
 F52 A:YUT401 0.0 56.8 1.0
C45 A:YUT401 1.3 51.5 1.0
F51 A:YUT401 2.2 41.4 1.0
PA5 A:YUT401 2.6 58.0 1.0
PB5 A:YUT401 2.6 51.3 1.0
O25 A:YUT401 2.8 56.5 1.0
O75 A:YUT401 2.9 58.1 1.0
O55 A:YUT401 3.1 52.9 1.0
CZ A:ARG89 3.1 40.5 1.0
NH2 A:ARG89 3.2 40.5 1.0
NE A:ARG89 3.3 33.6 1.0
O35 A:YUT401 3.6 62.0 1.0
NH1 A:ARG89 3.7 42.0 1.0
O15 A:YUT401 3.7 37.7 1.0
O65 A:YUT401 3.9 42.7 1.0
O36 A:YUT401 3.9 33.7 1.0
CD A:ARG89 4.1 28.5 1.0
O26 A:YUT401 4.8 39.5 1.0
PA6 A:YUT401 4.9 32.5 1.0
CG A:ARG89 5.0 26.8 1.0

Fluorine binding site 3 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F 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:F408

b:34.1
occ:1.00
 MG A:MG404 1.8 32.4 1.0
MG A:MG403 2.0 28.4 1.0
MG A:MG405 2.5 41.0 1.0
O A:HOH517 2.6 24.8 1.0
O A:HOH513 2.7 31.5 1.0
O A:HOH604 2.8 39.4 1.0
O A:HOH512 2.8 25.2 1.0
O A:HOH521 2.9 32.1 1.0
O A:HOH569 3.0 31.7 1.0
OE1 A:GLU66 3.1 20.6 1.0
OE2 A:GLU66 3.2 20.3 1.0
O A:HOH509 3.3 43.6 1.0
CD A:GLU66 3.6 19.1 1.0
O A:HOH507 3.7 47.0 1.0
OE2 A:GLU69 4.0 29.7 1.0
O A:HOH542 4.0 31.1 1.0
OE1 A:GLU70 4.2 19.2 1.0
O A:HOH515 4.4 40.9 1.0
MG A:MG402 4.5 21.4 1.0
O32 A:YUT401 4.6 22.2 1.0
CA A:GLY51 4.9 12.9 1.0
N A:GLY52 4.9 14.4 1.0
O23 A:YUT401 4.9 33.5 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 2 19:41:19 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