Chlorine 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:

Fluorine (F) 3 atoms
Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 8g9c

Go back to Chlorine Binding Sites List in 8g9c
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl406

b:18.4
occ:1.00
 O A:HOH508 3.1 17.1 1.0
O A:HOH579 3.1 17.9 1.0
ND2 A:ASN86 3.3 20.3 1.0
CE1 A:HIS91 3.6 16.0 1.0
NE2 A:GLN136 3.7 18.6 1.0
CG A:GLN136 3.7 12.0 1.0
CB A:VAL135 4.0 14.1 1.0
CB A:ASN86 4.2 14.9 1.0
CD A:LYS133 4.2 22.2 1.0
CD A:GLN136 4.2 13.6 1.0
CG A:ASN86 4.2 18.4 1.0
NE2 A:HIS91 4.3 17.4 1.0
N A:GLN136 4.5 12.9 1.0
CG1 A:VAL135 4.6 14.6 1.0
OH A:TYR139 4.6 13.8 1.0
CG2 A:VAL135 4.7 15.8 1.0
ND1 A:HIS91 4.7 15.6 1.0
CE A:LYS133 4.8 28.6 1.0
O A:HOH529 4.8 13.7 1.0
CA A:VAL135 4.9 13.1 1.0
CB A:GLN136 4.9 11.3 1.0
C A:VAL135 5.0 13.4 1.0

Chlorine binding site 2 out of 2 in 8g9c

Go back to Chlorine Binding Sites List in 8g9c
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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:Cl407

b:23.8
occ:1.00
 O A:HOH602 2.9 37.6 1.0
OG A:SER28 3.1 22.0 1.0
N A:GLU32 3.2 21.0 1.0
N A:GLU33 3.3 17.4 1.0
N A:SER28 3.3 17.2 1.0
N A:GLU31 3.7 22.3 1.0
OG A:SER30 3.7 24.5 0.5
CB A:SER28 3.8 21.8 1.0
CB A:ARG27 3.8 21.6 1.0
O A:SER28 3.8 19.9 1.0
O A:GLU33 3.9 15.3 1.0
N A:ARG27 3.9 16.2 1.0
CA A:GLU32 3.9 23.6 1.0
CA A:SER28 3.9 18.8 1.0
C A:GLU32 4.0 19.9 1.0
C A:GLU31 4.0 20.7 1.0
C A:ARG27 4.0 18.3 1.0
CB A:GLU32 4.0 27.8 1.0
CA A:GLU31 4.1 22.8 1.0
CA A:ARG27 4.1 18.9 1.0
CA A:GLU33 4.2 16.5 1.0
C A:SER28 4.2 21.1 1.0
CB A:GLU33 4.2 18.7 1.0
CB A:SER30 4.3 26.0 0.5
C A:SER30 4.3 25.5 1.0
C A:GLU33 4.5 15.4 1.0
CA A:SER30 4.7 22.7 0.5
N A:SER30 4.7 21.6 1.0
CG A:GLU33 4.7 25.8 1.0
CA A:SER30 4.8 23.3 0.5
CB A:PHE26 4.8 14.6 1.0
CB A:SER30 4.9 26.0 0.5
C A:PHE26 4.9 14.2 1.0
CG A:GLU32 4.9 33.0 1.0
CG A:ARG27 4.9 28.1 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: Tue Jul 30 09:54:04 2024

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