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Chlorine in PDB 8tf9: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi, PDB code: 8tf9 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) 35.94 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.995, 59.597, 62.695, 90, 90, 90
R / Rfree (%) 16.1 / 18.8

Other elements in 8tf9:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi 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 Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi (pdb code 8tf9). 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 Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi, PDB code: 8tf9:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8tf9

Go back to Chlorine Binding Sites List in 8tf9
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi


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-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:22.8
occ:1.00
 O A:HOH629 3.0 48.9 1.0
O A:HOH626 3.1 22.1 1.0
O A:HOH535 3.2 19.6 1.0
ND2 A:ASN86 3.3 27.3 1.0
NE2 A:GLN136 3.6 20.2 1.0
CE1 A:HIS91 3.7 22.0 1.0
CG A:GLN136 3.8 16.8 1.0
CB A:VAL135 4.0 18.5 1.0
CB A:ASN86 4.1 19.7 1.0
CD A:GLN136 4.2 18.7 1.0
CG A:ASN86 4.2 24.6 1.0
CD A:LYS133 4.3 22.5 1.0
NE2 A:HIS91 4.3 22.0 1.0
N A:GLN136 4.5 16.6 1.0
CG1 A:VAL135 4.6 17.8 1.0
CG2 A:VAL135 4.6 20.6 1.0
CE A:LYS133 4.7 25.9 1.0
O A:HOH637 4.7 32.5 1.0
ND1 A:HIS91 4.8 18.2 1.0
OH A:TYR139 4.8 17.0 1.0
O A:HOH550 4.8 17.6 1.0
CA A:VAL135 4.9 16.7 1.0
CB A:GLN136 4.9 17.0 1.0

Chlorine binding site 2 out of 2 in 8tf9

Go back to Chlorine Binding Sites List in 8tf9
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi


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 Myo-5-IP7, Produced Upon Myo-IP6 Phosphorylation By Tvi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:25.1
occ:1.00
 OG A:SER28 3.0 23.4 1.0
O A:HOH650 3.0 38.3 1.0
N A:GLU32 3.2 23.7 1.0
N A:SER28 3.3 21.5 1.0
N A:GLU33 3.4 18.8 1.0
N A:GLU31 3.7 22.6 1.0
O A:SER28 3.8 20.2 1.0
CB A:ARG27 3.8 25.6 1.0
CB A:SER28 3.8 24.9 1.0
N A:ARG27 3.8 19.7 1.0
O A:GLU33 3.9 20.1 1.0
CA A:SER28 3.9 23.1 1.0
CA A:GLU32 3.9 22.4 1.0
CB A:GLU32 4.0 25.7 1.0
C A:ARG27 4.0 22.3 1.0
CA A:ARG27 4.1 21.4 1.0
C A:GLU31 4.1 23.6 1.0
CA A:GLU31 4.1 22.6 1.0
C A:GLU32 4.1 21.4 1.0
C A:SER28 4.2 22.4 1.0
CA A:GLU33 4.2 19.4 1.0
CB A:GLU33 4.2 22.6 1.0
CB A:SER30 4.3 26.4 1.0
C A:SER30 4.4 24.4 1.0
C A:GLU33 4.6 18.5 1.0
N A:SER30 4.6 25.0 1.0
CA A:SER30 4.7 25.8 1.0
C A:PHE26 4.8 19.2 1.0
CB A:PHE26 4.8 19.6 1.0
CG A:GLU33 4.8 27.7 1.0
O A:HOH648 4.8 45.8 1.0
CG A:GLU32 4.9 31.9 1.0
O A:HOH501 4.9 38.5 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: Sun Jul 13 14:26:13 2025

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