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Chlorine in PDB 8tfa: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa was solved by G.Zong, H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.304, 59.64, 62.698, 90, 90, 90
R / Rfree (%) 15.4 / 16.9

Other elements in 8tfa:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk 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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk (pdb code 8tfa). 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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa:

Chlorine binding site 1 out of 1 in 8tfa

Go back to Chlorine Binding Sites List in 8tfa
Chlorine binding site 1 out of 1 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


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 Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:25.5
occ:1.00
 O A:HOH664 3.0 40.8 1.0
OG A:SER28 3.1 25.4 1.0
N A:GLU32 3.2 23.4 1.0
N A:SER28 3.3 22.1 1.0
N A:GLU33 3.4 20.8 1.0
OG A:SER30 3.6 33.9 0.5
N A:GLU31 3.6 24.3 1.0
O A:SER28 3.7 22.4 1.0
CB A:ARG27 3.7 27.2 1.0
CB A:SER28 3.8 24.8 1.0
N A:ARG27 3.8 19.9 1.0
O A:GLU33 3.9 20.8 1.0
CA A:GLU32 3.9 22.9 1.0
CA A:SER28 3.9 22.8 1.0
CB A:GLU32 4.0 27.1 1.0
C A:ARG27 4.0 23.5 1.0
CA A:GLU31 4.0 24.2 1.0
C A:GLU31 4.0 23.0 1.0
CA A:ARG27 4.1 22.2 1.0
C A:GLU32 4.1 23.6 1.0
C A:SER28 4.1 23.3 1.0
CA A:GLU33 4.2 20.6 1.0
CB A:SER30 4.3 25.9 0.5
CB A:GLU33 4.3 22.7 1.0
C A:SER30 4.3 26.8 0.5
C A:SER30 4.4 25.2 0.5
C A:GLU33 4.5 18.9 1.0
N A:SER30 4.6 24.7 0.5
CA A:SER30 4.6 25.2 0.5
N A:SER30 4.7 26.8 0.5
CB A:SER30 4.8 31.0 0.5
CB A:PHE26 4.8 21.3 1.0
O A:HOH663 4.8 44.6 1.0
CA A:SER30 4.8 28.6 0.5
C A:PHE26 4.8 19.9 1.0
CG A:GLU33 4.8 27.7 1.0
CG A:GLU32 4.8 31.4 1.0
CG A:ARG27 4.9 31.6 1.0

Reference:

G.Zong, H.Wang, S.B.Shears. Biochemical and Structural Characterization of A Giant Virus Inositol Pyrophosphate Kinase Embo J. 2023.
ISSN: ESSN 1460-2075
Page generated: Thu Dec 28 03:32:23 2023

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