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Chlorine in PDB 6wod: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride.

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride.

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride.:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride., PDB code: 6wod was solved by G.N.Zong, H.C.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.77 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.224, 59.605, 62.719, 90, 90, 90
R / Rfree (%) 13.3 / 15.6

Other elements in 6wod:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride. (pdb code 6wod). 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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride., PDB code: 6wod:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6wod

Go back to Chlorine Binding Sites List in 6wod
Chlorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride.


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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:15.3
occ:1.00
 O A:HOH684 2.9 37.8 1.0
O A:HOH631 3.1 12.9 1.0
O A:HOH714 3.2 15.4 1.0
ND2 A:ASN86 3.3 17.9 1.0
CE1 A:HIS91 3.7 13.1 1.0
NE2 A:GLN136 3.7 15.0 1.0
CG A:GLN136 3.8 10.6 1.0
CB A:VAL135 4.0 12.7 1.0
CB A:ASN86 4.1 13.4 1.0
CG A:ASN86 4.2 14.9 1.0
CD A:LYS133 4.2 14.2 0.5
CD A:GLN136 4.2 11.0 1.0
CD A:LYS133 4.3 13.7 0.5
NE2 A:HIS91 4.3 14.5 1.0
N A:GLN136 4.5 10.1 1.0
CG1 A:VAL135 4.5 12.9 1.0
CG2 A:VAL135 4.6 13.8 1.0
OH A:TYR139 4.8 10.7 1.0
O A:HOH645 4.8 10.3 1.0
NZ A:LYS133 4.8 18.2 0.5
ND1 A:HIS91 4.8 11.4 1.0
CE A:LYS133 4.8 15.5 0.5
CA A:VAL135 4.9 12.7 1.0
C A:VAL135 5.0 13.2 1.0
CB A:GLN136 5.0 10.6 1.0

Chlorine binding site 2 out of 2 in 6wod

Go back to Chlorine Binding Sites List in 6wod
Chlorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride.


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 Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 2MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:17.8
occ:1.00
 O A:HOH664 3.0 33.4 1.0
OG A:SER28 3.1 18.5 1.0
N A:GLU32 3.2 15.7 1.0
OG A:SER30 3.2 21.7 0.3
N A:SER28 3.2 14.1 1.0
N A:GLU33 3.3 13.8 0.5
N A:GLU33 3.3 13.1 0.5
N A:GLU31 3.6 16.7 1.0
O A:SER28 3.7 14.8 1.0
CB A:ARG27 3.8 18.0 1.0
N A:ARG27 3.8 12.0 1.0
O A:GLU33 3.8 10.7 0.5
O A:GLU33 3.9 11.6 0.5
CB A:SER28 3.9 18.1 1.0
CA A:SER28 3.9 16.0 1.0
CA A:GLU32 3.9 16.5 1.0
CA A:GLU31 4.0 16.6 1.0
C A:ARG27 4.0 14.1 1.0
CB A:GLU32 4.0 19.7 1.0
C A:GLU31 4.0 16.3 1.0
CA A:ARG27 4.0 14.2 1.0
C A:GLU32 4.1 14.1 1.0
C A:SER28 4.1 16.6 1.0
CA A:GLU33 4.2 13.6 0.5
CB A:GLU33 4.2 16.2 0.5
CA A:GLU33 4.2 12.6 0.5
CB A:GLU33 4.3 14.5 0.5
C A:SER30 4.4 18.6 1.0
CB A:SER30 4.4 21.6 0.7
C A:GLU33 4.5 11.5 0.5
CB A:SER30 4.5 20.5 0.3
C A:GLU33 4.5 11.2 0.5
CB A:PHE26 4.6 12.3 1.0
N A:SER30 4.6 19.1 1.0
C A:PHE26 4.7 10.9 1.0
CA A:SER30 4.7 20.7 0.7
CA A:SER30 4.7 20.4 0.3
CG A:GLU33 4.9 17.5 0.5
O A:HOH753 4.9 41.8 1.0
CG A:GLU32 4.9 23.5 1.0
CG A:GLU33 4.9 19.3 0.5
CA A:PHE26 5.0 11.0 1.0

Reference:

G.Zong, N.Jork, S.Hostachy, D.Fiedler, H.J.Jessen, S.B.Shears, H.Wang. New Structural Insights Reveal An Expanded Reaction Cycle For Inositol Pyrophosphate Hydrolysis By Human DIPP1. Faseb J. V. 35 21275 2021.
ISSN: ESSN 1530-6860
PubMed: 33475202
DOI: 10.1096/FJ.202001489R
Page generated: Mon Jul 29 16:49:41 2024

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