Atomistry » Chlorine » PDB 6wji-6wu8 » 6woi
Atomistry »
  Chlorine »
    PDB 6wji-6wu8 »
      6woi »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy