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Chlorine in PDB 6woi: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds, PDB code: 6woi 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) 31.63 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.503, 59.608, 62.353, 90, 90, 90
R / Rfree (%) 14.5 / 16.7

Other elements in 6woi:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds (pdb code 6woi). 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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds, PDB code: 6woi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6woi

Go back to Chlorine Binding Sites List in 6woi
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds


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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:21.1
occ:1.00
 O A:HOH595 3.0 22.4 1.0
O A:HOH531 3.1 19.4 1.0
ND2 A:ASN86 3.3 19.4 1.0
CE1 A:HIS91 3.6 17.9 1.0
NE2 A:GLN136 3.7 13.7 1.0
CG A:GLN136 3.7 10.5 1.0
CB A:VAL135 4.1 13.9 1.0
CD A:LYS133 4.2 15.8 1.0
CD A:GLN136 4.2 11.2 1.0
NE2 A:HIS91 4.2 17.0 1.0
CG A:ASN86 4.2 14.9 1.0
CB A:ASN86 4.2 13.7 1.0
N A:GLN136 4.5 10.0 1.0
CG1 A:VAL135 4.6 13.8 1.0
CE A:LYS133 4.6 21.2 1.0
OH A:TYR139 4.7 10.3 1.0
ND1 A:HIS91 4.7 16.2 1.0
O A:HOH609 4.7 29.0 1.0
CG2 A:VAL135 4.7 14.6 1.0
O A:HOH532 4.8 12.7 1.0
CB A:GLN136 4.9 10.1 1.0
CA A:VAL135 4.9 13.6 1.0
C A:VAL135 5.0 11.2 1.0

Chlorine binding site 2 out of 2 in 6woi

Go back to Chlorine Binding Sites List in 6woi
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds


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 1-Diphosphoinositol Pentakisphosphate, Mg, and Fluoride Ion, Presoaked with 1,5-IP8, Mg and Fluoride For 30 Seconds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:19.1
occ:1.00
 O A:HOH606 3.1 40.8 1.0
OG A:SER28 3.1 19.4 1.0
N A:GLU32 3.1 16.5 1.0
N A:SER28 3.3 15.7 1.0
N A:GLU33 3.3 13.0 1.0
OG A:SER30 3.6 23.3 0.5
N A:GLU31 3.7 17.4 1.0
N A:ARG27 3.7 11.7 1.0
O A:SER28 3.7 17.0 1.0
CB A:ARG27 3.8 17.5 1.0
O A:GLU33 3.8 11.8 1.0
CB A:SER28 3.9 19.1 1.0
CA A:GLU32 3.9 17.3 1.0
CA A:SER28 3.9 18.3 1.0
CB A:GLU32 4.0 22.5 1.0
C A:ARG27 4.0 15.2 1.0
CA A:ARG27 4.0 13.9 1.0
CA A:GLU31 4.0 16.6 1.0
C A:GLU31 4.0 15.1 1.0
C A:GLU32 4.1 13.9 1.0
C A:SER28 4.2 18.2 1.0
CA A:GLU33 4.2 12.7 1.0
CB A:GLU33 4.2 15.8 1.0
C A:SER30 4.4 20.1 1.0
C A:GLU33 4.5 11.2 1.0
CB A:SER30 4.5 19.7 0.5
CB A:PHE26 4.6 10.6 1.0
C A:PHE26 4.7 10.3 1.0
N A:SER30 4.8 20.0 1.0
CG A:GLU33 4.8 21.8 1.0
CA A:SER30 4.8 19.7 0.5
CB A:SER30 4.8 21.7 0.5
CG A:GLU32 4.9 28.2 1.0
CA A:SER30 4.9 19.9 0.5
CG A:ARG27 4.9 23.2 1.0
CA A:PHE26 5.0 10.0 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: Mon Jul 29 16:50:22 2024

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