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: Tue Jul 30 12:48:06 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy