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Chlorine in PDB 6woc: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.

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

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride., PDB code: 6woc 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) 31.40 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.708, 59.611, 62.581, 90, 90, 90
R / Rfree (%) 13.8 / 16.4

Other elements in 6woc:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. also contains other interesting chemical elements:

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 and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. (pdb code 6woc). 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 and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride., PDB code: 6woc:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6woc

Go back to Chlorine Binding Sites List in 6woc
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.


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 and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:14.9
occ:1.00
 O A:HOH621 3.0 38.2 1.0
O A:HOH515 3.2 13.2 1.0
O A:HOH596 3.2 15.4 1.0
ND2 A:ASN86 3.3 17.7 1.0
CE1 A:HIS91 3.7 12.9 1.0
NE2 A:GLN136 3.7 15.2 1.0
CG A:GLN136 3.8 10.8 1.0
CB A:VAL135 4.0 13.4 1.0
CB A:ASN86 4.1 12.7 1.0
CD A:LYS133 4.2 14.1 1.0
CG A:ASN86 4.2 14.2 1.0
CD A:GLN136 4.2 11.0 1.0
NE2 A:HIS91 4.3 13.2 1.0
N A:GLN136 4.5 10.7 1.0
CG1 A:VAL135 4.5 13.0 1.0
CG2 A:VAL135 4.7 14.4 1.0
O A:HOH535 4.8 10.6 1.0
OH A:TYR139 4.8 10.1 1.0
ND1 A:HIS91 4.8 11.2 1.0
CE A:LYS133 4.8 18.2 1.0
CA A:VAL135 4.9 13.8 1.0
CB A:GLN136 5.0 11.0 1.0
C A:VAL135 5.0 12.6 1.0

Chlorine binding site 2 out of 2 in 6woc

Go back to Chlorine Binding Sites List in 6woc
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol Pentakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride.


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 and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 1MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:17.8
occ:1.00
 O A:HOH642 3.0 33.5 1.0
OG A:SER28 3.1 18.7 1.0
N A:GLU32 3.2 15.1 1.0
OG A:SER30 3.2 25.2 0.5
N A:SER28 3.2 13.5 1.0
N A:GLU33 3.3 12.3 1.0
CB A:ARG27 3.6 16.4 1.0
N A:GLU31 3.6 16.5 1.0
O A:SER28 3.7 14.4 1.0
N A:ARG27 3.8 11.6 1.0
O A:GLU33 3.8 12.2 1.0
CB A:SER28 3.9 17.4 1.0
CA A:GLU32 3.9 16.1 1.0
CA A:SER28 3.9 15.2 1.0
CB A:GLU32 4.0 19.6 1.0
C A:ARG27 4.0 13.6 1.0
CA A:ARG27 4.0 13.2 1.0
CA A:GLU31 4.0 15.9 1.0
C A:GLU31 4.1 15.6 1.0
C A:GLU32 4.1 13.8 1.0
C A:SER28 4.1 16.1 1.0
CA A:GLU33 4.2 12.9 1.0
CB A:GLU33 4.3 15.3 1.0
C A:SER30 4.4 18.5 1.0
CB A:SER30 4.4 19.4 0.5
CB A:SER30 4.5 21.9 0.5
C A:GLU33 4.5 10.7 1.0
CB A:PHE26 4.6 12.4 1.0
N A:SER30 4.7 19.2 1.0
CA A:SER30 4.7 19.8 0.5
CG A:ARG27 4.7 22.7 1.0
C A:PHE26 4.7 11.0 1.0
CA A:SER30 4.7 20.5 0.5
O A:HOH644 4.8 46.2 1.0
CG A:GLU33 4.9 19.1 1.0
CG A:GLU32 4.9 23.9 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 16:49:41 2024

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