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Chlorine in PDB 6wo8: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion, PDB code: 6wo8 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) 43.01 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.28, 59.48, 62.26, 90, 90, 90
R / Rfree (%) 14.9 / 21.6

Other elements in 6wo8:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion (pdb code 6wo8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion, PDB code: 6wo8:

Chlorine binding site 1 out of 1 in 6wo8

Go back to Chlorine Binding Sites List in 6wo8
Chlorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5-Diphosphoinositol 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), 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 1,3,4,6-Tetrakisphosphate (5-Pp- IP4), Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:36.9
occ:1.00
 O A:HOH615 2.7 33.1 1.0
OG A:SER28 3.0 24.1 1.0
N A:GLU32 3.0 22.2 1.0
N A:SER28 3.2 19.1 1.0
N A:GLU33 3.3 17.5 1.0
OG A:SER30 3.4 31.0 1.0
N A:GLU31 3.5 20.7 1.0
O A:SER28 3.5 18.3 1.0
O A:GLU33 3.8 15.8 1.0
CA A:GLU32 3.8 19.3 1.0
CB A:SER28 3.8 23.1 1.0
N A:ARG27 3.8 19.3 1.0
CA A:SER28 3.8 19.9 1.0
C A:GLU31 3.9 23.3 1.0
CA A:GLU31 3.9 21.9 1.0
CB A:GLU32 3.9 20.9 1.0
CB A:ARG27 4.0 23.7 1.0
C A:ARG27 4.0 21.2 1.0
C A:GLU32 4.0 18.8 1.0
C A:SER28 4.0 18.9 1.0
CA A:ARG27 4.1 20.0 1.0
C A:SER30 4.2 19.4 1.0
CA A:GLU33 4.2 17.6 1.0
CB A:GLU33 4.3 21.1 1.0
C A:GLU33 4.5 14.9 1.0
N A:SER30 4.5 22.8 1.0
CB A:SER30 4.5 26.7 1.0
O A:HOH635 4.6 46.3 1.0
CA A:SER30 4.6 23.9 1.0
CB A:PHE26 4.7 18.8 1.0
C A:PHE26 4.7 18.5 1.0
CG A:GLU32 4.8 26.5 1.0
CG A:GLU33 5.0 24.8 1.0
O A:SER30 5.0 25.1 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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