Chlorine in PDB 8t98: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

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

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98 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) 36.49 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.103, 59.571, 62.43, 90, 90, 90
R / Rfree (%) 14.9 / 17.2

Other elements in 8t98:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion (pdb code 8t98). 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-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8t98

Go back to Chlorine Binding Sites List in 8t98
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:15.7
occ:1.00
 O A:HOH664 3.0 23.4 1.0
O A:HOH638 3.1 15.0 1.0
O A:HOH521 3.1 14.2 1.0
ND2 A:ASN86 3.3 17.5 1.0
CE1 A:HIS91 3.6 13.9 1.0
CG A:GLN136 3.7 10.2 1.0
NE2 A:GLN136 3.7 14.9 1.0
CB A:VAL135 4.0 12.3 1.0
CD A:LYS133 4.1 14.4 1.0
CD A:GLN136 4.2 12.2 1.0
NE2 A:HIS91 4.3 14.2 1.0
CB A:ASN86 4.3 13.8 1.0
CG A:ASN86 4.3 16.9 1.0
O A:HOH652 4.4 41.3 1.0
N A:GLN136 4.4 10.3 1.0
CG1 A:VAL135 4.5 13.5 1.0
CG2 A:VAL135 4.7 12.6 1.0
CE A:LYS133 4.7 16.2 1.0
OH A:TYR139 4.7 11.6 1.0
ND1 A:HIS91 4.7 12.7 1.0
O A:HOH545 4.7 10.8 1.0
CA A:VAL135 4.9 11.1 1.0
O A:HOH688 4.9 25.5 1.0
CB A:GLN136 4.9 10.2 1.0
C A:VAL135 4.9 10.4 1.0

Chlorine binding site 2 out of 2 in 8t98

Go back to Chlorine Binding Sites List in 8t98
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:18.0
occ:1.00
 O A:HOH704 3.0 29.9 1.0
OG A:SER28 3.1 17.1 1.0
N A:GLU32 3.1 15.2 1.0
N A:SER28 3.3 14.6 1.0
N A:GLU33 3.3 13.5 1.0
OG A:SER30 3.6 26.2 0.5
N A:GLU31 3.6 16.1 1.0
O A:SER28 3.7 14.7 1.0
CB A:ARG27 3.8 17.9 1.0
N A:ARG27 3.8 13.1 1.0
CB A:SER28 3.8 17.1 1.0
O A:GLU33 3.9 13.3 1.0
CA A:GLU32 3.9 16.6 1.0
CA A:SER28 3.9 15.8 1.0
CB A:GLU32 4.0 19.0 1.0
C A:ARG27 4.0 15.9 1.0
C A:GLU31 4.0 16.4 1.0
CA A:GLU31 4.0 16.8 1.0
C A:GLU32 4.0 15.7 1.0
CA A:ARG27 4.1 14.6 1.0
C A:SER28 4.1 16.8 1.0
CA A:GLU33 4.2 13.4 1.0
CB A:SER30 4.3 18.0 0.5
CB A:GLU33 4.3 14.4 1.0
C A:SER30 4.4 18.1 1.0
C A:GLU33 4.5 12.5 1.0
CA A:SER30 4.7 17.8 0.5
N A:SER30 4.7 18.0 1.0
CB A:PHE26 4.7 13.1 1.0
CB A:SER30 4.7 22.3 0.5
O A:HOH702 4.7 35.1 1.0
C A:PHE26 4.8 12.3 1.0
O A:HOH682 4.8 45.3 1.0
CA A:SER30 4.8 19.8 0.5
CG A:GLU33 4.8 20.7 1.0
CG A:GLU32 4.9 24.4 1.0
O A:HOH502 4.9 24.8 1.0
CG A:ARG27 4.9 22.1 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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