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Chlorine 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:

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

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 6wob

Go back to Chlorine Binding Sites List in 6wob
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl405

b:13.8
occ:1.00
 O A:HOH601 3.1 21.8 1.0
O A:HOH520 3.2 13.9 1.0
O A:HOH588 3.2 16.2 1.0
ND2 A:ASN86 3.3 16.2 1.0
NE2 A:GLN136 3.7 14.1 1.0
CG A:GLN136 3.7 11.9 1.0
CE1 A:HIS91 3.8 13.7 1.0
CB A:VAL135 4.0 16.5 1.0
CB A:ASN86 4.1 12.9 1.0
CD A:LYS133 4.2 17.6 1.0
CG A:ASN86 4.2 13.6 1.0
CD A:GLN136 4.2 12.8 1.0
O A:HOH564 4.4 26.2 1.0
N A:GLN136 4.5 12.7 1.0
CG1 A:VAL135 4.5 15.3 1.0
NE2 A:HIS91 4.5 13.4 1.0
O A:HOH607 4.6 16.1 1.0
CG2 A:VAL135 4.7 18.3 1.0
O A:HOH527 4.7 25.5 1.0
ND1 A:HIS91 4.8 13.8 1.0
CE A:LYS133 4.8 18.6 1.0
CA A:VAL135 4.8 15.3 1.0
OH A:TYR139 4.9 10.6 1.0
CB A:GLN136 4.9 11.8 1.0
C A:VAL135 4.9 15.6 1.0
N A:VAL135 4.9 16.0 1.0

Chlorine binding site 2 out of 2 in 6wob

Go back to Chlorine Binding Sites List in 6wob
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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:Cl406

b:27.6
occ:1.00
 OG A:SER28 3.0 27.0 1.0
N A:GLU32 3.1 20.4 1.0
N A:GLU33 3.3 14.5 1.0
N A:SER28 3.3 19.5 1.0
OG A:SER30 3.3 30.8 0.5
N A:GLU31 3.6 21.2 1.0
O A:SER28 3.6 22.3 1.0
O A:GLU33 3.8 12.5 1.0
N A:ARG27 3.8 15.0 1.0
CB A:SER28 3.8 25.6 1.0
CA A:GLU32 3.9 20.0 1.0
CA A:SER28 3.9 24.9 1.0
CB A:ARG27 3.9 19.6 1.0
CA A:GLU31 4.0 22.5 1.0
C A:GLU31 4.0 21.1 1.0
C A:ARG27 4.0 18.5 1.0
C A:GLU32 4.0 16.6 1.0
CB A:GLU32 4.0 24.6 1.0
C A:SER28 4.1 25.3 1.0
CA A:ARG27 4.1 16.7 1.0
CA A:GLU33 4.1 13.5 1.0
CB A:GLU33 4.2 16.4 1.0
C A:SER30 4.3 25.2 1.0
CB A:SER30 4.4 27.3 0.5
C A:GLU33 4.4 11.3 1.0
CB A:SER30 4.5 30.2 0.5
CB A:PHE26 4.6 13.8 1.0
N A:SER30 4.6 27.2 1.0
CA A:SER30 4.7 26.7 0.5
C A:PHE26 4.7 12.8 1.0
CA A:SER30 4.7 27.0 0.5
CG A:GLU33 4.9 22.2 1.0
CG A:GLU32 4.9 30.7 1.0
CA A:PHE26 5.0 12.4 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: Sat Jul 12 21:20:16 2025

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