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Chlorine in PDB 6wo7: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion, PDB code: 6wo7 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) 43.13 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.365, 59.602, 62.493, 90, 90, 90
R / Rfree (%) 13.9 / 16.8

Other elements in 6wo7:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion 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 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion (pdb code 6wo7). 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-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion, PDB code: 6wo7:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6wo7

Go back to Chlorine Binding Sites List in 6wo7
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-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 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:14.3
occ:1.00
 O A:HOH530 3.2 12.8 1.0
O A:HOH617 3.2 15.4 1.0
ND2 A:ASN86 3.3 17.8 1.0
CE1 A:HIS91 3.7 11.4 1.0
NE2 A:GLN136 3.8 14.0 1.0
CG A:GLN136 3.8 10.2 1.0
CB A:VAL135 4.0 11.7 1.0
CB A:ASN86 4.1 12.1 1.0
CD A:LYS133 4.2 13.1 1.0
CG A:ASN86 4.2 14.8 1.0
CD A:GLN136 4.3 10.4 1.0
NE2 A:HIS91 4.3 12.1 1.0
CG1 A:VAL135 4.5 11.5 1.0
N A:GLN136 4.5 9.5 1.0
CG2 A:VAL135 4.6 12.4 1.0
CE A:LYS133 4.7 16.8 1.0
O A:HOH549 4.7 11.5 1.0
ND1 A:HIS91 4.8 10.6 1.0
OH A:TYR139 4.8 9.2 1.0
CA A:VAL135 4.9 11.8 1.0
C A:VAL135 5.0 10.4 1.0

Chlorine binding site 2 out of 2 in 6wo7

Go back to Chlorine Binding Sites List in 6wo7
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate (5-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 5-Diphosphoinositol Pentakisphosphate (5-IP7), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:18.9
occ:1.00
 O A:HOH505 3.0 26.2 1.0
OG A:SER28 3.0 19.1 1.0
N A:GLU32 3.1 15.6 1.0
N A:SER28 3.2 13.9 1.0
OG A:SER30 3.3 24.0 0.5
N A:GLU33 3.3 12.4 1.0
N A:GLU31 3.6 15.7 1.0
O A:SER28 3.6 14.5 1.0
N A:ARG27 3.8 11.2 1.0
CB A:SER28 3.8 16.4 1.0
CB A:ARG27 3.8 17.0 1.0
O A:GLU33 3.8 11.0 1.0
CA A:SER28 3.9 14.7 1.0
CA A:GLU32 3.9 16.5 1.0
CB A:GLU32 3.9 18.9 1.0
C A:ARG27 4.0 13.9 1.0
CA A:GLU31 4.0 16.0 1.0
C A:GLU31 4.0 15.6 1.0
CA A:ARG27 4.0 12.9 1.0
C A:GLU32 4.1 13.8 1.0
C A:SER28 4.1 14.7 1.0
CA A:GLU33 4.2 12.5 1.0
CB A:GLU33 4.2 15.4 1.0
C A:SER30 4.3 17.5 1.0
CB A:SER30 4.4 19.2 0.5
C A:GLU33 4.5 10.7 1.0
CB A:SER30 4.5 21.1 0.5
N A:SER30 4.6 18.7 1.0
CB A:PHE26 4.6 12.0 1.0
CA A:SER30 4.7 18.8 0.5
C A:PHE26 4.7 10.6 1.0
CA A:SER30 4.7 19.1 0.5
CG A:GLU33 4.8 19.4 1.0
O A:HOH651 4.8 35.6 1.0
CG A:GLU32 4.9 23.4 1.0
OE2 A:GLU33 4.9 33.9 1.0
CG A:ARG27 5.0 21.1 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 16:48:21 2024

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