Chlorine in PDB 8t99: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion, PDB code: 8t99 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) 31.45 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.824, 59.634, 62.653, 90, 90, 90
R / Rfree (%) 15.6 / 18.3

Other elements in 8t99:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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 Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion (pdb code 8t99). 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 Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion, PDB code: 8t99:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8t99

Go back to Chlorine Binding Sites List in 8t99
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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 Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:17.2
occ:1.00
 O A:HOH638 3.1 16.1 1.0
O A:HOH531 3.2 15.7 1.0
ND2 A:ASN86 3.2 18.4 1.0
O A:HOH641 3.2 26.7 1.0
NE2 A:GLN136 3.6 15.8 1.0
CE1 A:HIS91 3.6 15.6 1.0
CG A:GLN136 3.8 11.2 1.0
CB A:VAL135 4.1 13.0 1.0
CD A:LYS133 4.1 17.3 1.0
CD A:GLN136 4.2 13.5 1.0
CB A:ASN86 4.2 15.3 1.0
CG A:ASN86 4.2 18.5 1.0
NE2 A:HIS91 4.2 16.2 1.0
N A:GLN136 4.6 12.8 1.0
CE A:LYS133 4.6 19.5 1.0
CG1 A:VAL135 4.7 12.9 1.0
OH A:TYR139 4.7 12.2 1.0
ND1 A:HIS91 4.8 15.6 1.0
CG2 A:VAL135 4.8 14.6 1.0
O A:HOH558 4.8 12.1 1.0
O A:HOH665 4.8 27.1 1.0
CA A:VAL135 4.9 11.6 1.0
CB A:GLN136 5.0 11.6 1.0

Chlorine binding site 2 out of 2 in 8t99

Go back to Chlorine Binding Sites List in 8t99
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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 Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:21.3
occ:1.00
 O A:HOH677 2.9 33.9 1.0
OG A:SER28 3.0 18.9 1.0
N A:GLU32 3.2 19.1 1.0
N A:SER28 3.3 16.8 1.0
N A:GLU33 3.3 14.6 1.0
OG A:SER30 3.5 26.6 0.5
N A:GLU31 3.7 19.0 1.0
O A:SER28 3.7 17.1 1.0
CB A:SER28 3.8 19.0 1.0
CB A:ARG27 3.8 19.1 1.0
N A:ARG27 3.8 14.8 1.0
O A:GLU33 3.8 14.4 1.0
CA A:GLU32 3.9 18.5 1.0
CA A:SER28 3.9 17.9 1.0
C A:ARG27 4.0 17.9 1.0
CB A:GLU32 4.0 22.2 1.0
C A:GLU31 4.1 19.3 1.0
CA A:ARG27 4.1 15.8 1.0
C A:GLU32 4.1 18.6 1.0
CA A:GLU31 4.1 18.1 1.0
C A:SER28 4.1 17.9 1.0
CA A:GLU33 4.2 13.8 1.0
CB A:GLU33 4.3 16.4 1.0
CB A:SER30 4.3 21.3 0.5
C A:SER30 4.4 20.6 1.0
C A:GLU33 4.5 13.0 1.0
N A:SER30 4.6 20.3 1.0
CB A:SER30 4.7 23.6 0.5
CA A:SER30 4.7 20.6 0.5
CB A:PHE26 4.7 14.7 1.0
CA A:SER30 4.7 22.1 0.5
C A:PHE26 4.8 14.1 1.0
O A:HOH676 4.8 35.9 1.0
CG A:GLU33 4.8 21.0 1.0
CG A:GLU32 4.9 25.6 1.0
CG A:ARG27 4.9 24.4 1.0
O A:HOH501 4.9 33.2 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: Tue Jul 30 12:44:39 2024

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