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Chlorine in PDB 7tn4: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4 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) 31.40 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.149, 59.743, 62.769, 90, 90, 90
R / Rfree (%) 18.3 / 21.7

Other elements in 7tn4:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion (pdb code 7tn4). 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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion, PDB code: 7tn4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7tn4

Go back to Chlorine Binding Sites List in 7tn4
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:18.5
occ:1.00
 O A:HOH613 3.1 16.0 1.0
O A:HOH683 3.1 17.5 1.0
ND2 A:ASN86 3.3 18.1 1.0
NE2 A:GLN136 3.6 15.7 1.0
CE1 A:HIS91 3.7 15.9 1.0
CG A:GLN136 3.7 13.3 1.0
CB A:VAL135 4.0 15.1 1.0
CB A:ASN86 4.1 15.5 1.0
CD A:GLN136 4.1 14.8 1.0
NE2 A:HIS91 4.2 14.9 1.0
CG A:ASN86 4.2 17.1 1.0
CD A:LYS133 4.2 20.1 1.0
N A:GLN136 4.6 13.6 1.0
CG1 A:VAL135 4.6 15.4 1.0
CE A:LYS133 4.6 25.4 1.0
OH A:TYR139 4.7 12.3 1.0
CG2 A:VAL135 4.7 15.4 1.0
O A:HOH631 4.7 9.3 1.0
ND1 A:HIS91 4.8 13.6 1.0
CB A:GLN136 4.9 13.3 1.0
CA A:VAL135 4.9 14.1 1.0

Chlorine binding site 2 out of 2 in 7tn4

Go back to Chlorine Binding Sites List in 7tn4
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-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 2 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 3-Diphosphoinositol 1,2,4,5-Tetrakisphosphate (3-Pp- IP4), Mg and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:21.6
occ:1.00
 OG A:SER28 3.0 17.6 1.0
O A:HOH712 3.0 29.1 1.0
N A:GLU32 3.1 17.9 1.0
N A:SER28 3.2 16.9 1.0
N A:GLU33 3.4 16.3 1.0
OG A:SER30 3.5 25.7 0.5
N A:GLU31 3.7 19.4 1.0
O A:SER28 3.7 16.0 1.0
CB A:SER28 3.8 19.7 1.0
O A:GLU33 3.9 13.7 1.0
N A:ARG27 3.9 14.9 1.0
CA A:SER28 3.9 18.9 1.0
CB A:ARG27 3.9 21.3 1.0
CA A:GLU32 3.9 18.4 1.0
C A:ARG27 3.9 18.3 1.0
CA A:GLU31 4.0 19.5 1.0
C A:GLU31 4.0 17.3 1.0
CB A:GLU32 4.0 21.0 1.0
CA A:ARG27 4.1 16.7 1.0
C A:GLU32 4.1 17.6 1.0
C A:SER28 4.1 19.0 1.0
CB A:GLU33 4.3 19.6 1.0
CA A:GLU33 4.3 16.5 1.0
C A:SER30 4.4 20.2 1.0
C A:GLU33 4.6 14.7 1.0
CB A:SER30 4.6 17.9 0.5
O A:HOH716 4.7 32.7 1.0
CG A:GLU32 4.7 26.9 1.0
N A:SER30 4.7 19.8 1.0
CB A:SER30 4.7 22.4 0.5
CA A:SER30 4.8 19.3 0.5
CA A:SER30 4.8 21.5 0.5
CB A:PHE26 4.8 14.6 1.0
C A:PHE26 4.8 13.8 1.0
CG A:GLU33 4.9 25.7 1.0
O A:ARG27 5.0 18.0 1.0
O A:HOH608 5.0 22.5 1.0

Reference:

G.Zong, S.B.Shears, H.Wang. Structural and Catalytic Analyses of the Insp 6 Kinase Activities of Higher Plant Itpks. Faseb J. V. 36 22380 2022.
ISSN: ESSN 1530-6860
PubMed: 35635723
DOI: 10.1096/FJ.202200393R
Page generated: Sun Jul 13 07:31:20 2025

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