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Chlorine in PDB 6wof: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN 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 20MIN 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 20MIN 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 20MIN in the Absence of Fluoride., PDB code: 6wof 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) 27.79 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.062, 59.827, 62.729, 90, 90, 90
R / Rfree (%) 12.3 / 14.8

Other elements in 6wof:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 20MIN in the Absence of Fluoride. also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

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 20MIN in the Absence of Fluoride. (pdb code 6wof). 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 20MIN in the Absence of Fluoride., PDB code: 6wof:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6wof

Go back to Chlorine Binding Sites List in 6wof
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 20MIN 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 20MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:14.7
occ:1.00
 O A:HOH618 3.1 12.3 1.0
O A:HOH707 3.2 15.7 1.0
ND2 A:ASN86 3.3 19.0 1.0
NE2 A:GLN136 3.7 13.3 1.0
CE1 A:HIS91 3.7 13.8 1.0
CG A:GLN136 3.8 9.2 1.0
CB A:VAL135 4.0 10.1 1.0
CB A:ASN86 4.1 13.0 1.0
CG A:ASN86 4.2 15.4 1.0
CD A:GLN136 4.2 10.8 1.0
CD A:LYS133 4.3 15.6 1.0
NE2 A:HIS91 4.4 14.9 1.0
N A:GLN136 4.6 9.1 1.0
CG1 A:VAL135 4.6 10.8 1.0
CG2 A:VAL135 4.7 11.1 1.0
OH A:TYR139 4.8 10.3 1.0
CE A:LYS133 4.8 21.0 1.0
ND1 A:HIS91 4.8 11.5 1.0
O A:HOH636 4.8 10.2 1.0
O A:HOH726 4.8 37.2 1.0
CA A:VAL135 4.9 9.6 1.0
CB A:GLN136 5.0 8.8 1.0

Chlorine binding site 2 out of 2 in 6wof

Go back to Chlorine Binding Sites List in 6wof
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 20MIN 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 20MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:16.3
occ:1.00
 O A:HOH720 3.0 36.9 1.0
OG A:SER28 3.2 17.0 1.0
OG A:SER30 3.2 18.6 0.2
N A:GLU32 3.2 15.1 1.0
N A:SER28 3.3 12.9 1.0
N A:GLU33 3.3 13.7 0.3
N A:GLU33 3.4 13.6 0.7
CB A:ARG27 3.7 16.6 1.0
O A:SER28 3.7 14.4 1.0
N A:GLU31 3.7 16.1 1.0
N A:ARG27 3.8 11.1 1.0
O A:GLU33 3.9 11.8 0.3
O A:GLU33 3.9 11.5 0.7
CB A:SER28 3.9 16.9 1.0
CA A:GLU32 4.0 15.4 1.0
CA A:SER28 4.0 15.0 1.0
CB A:GLU32 4.0 17.4 1.0
CA A:ARG27 4.1 12.4 1.0
C A:ARG27 4.1 12.4 1.0
CA A:GLU31 4.1 15.8 1.0
C A:GLU31 4.1 16.2 1.0
C A:GLU32 4.1 14.4 1.0
C A:SER28 4.2 14.8 1.0
CB A:GLU33 4.2 13.9 0.3
CA A:GLU33 4.2 13.1 0.3
CA A:GLU33 4.2 13.2 0.7
CB A:GLU33 4.3 14.3 0.7
CB A:SER30 4.4 18.9 0.8
C A:SER30 4.4 18.2 1.0
CB A:SER30 4.5 18.4 0.2
C A:GLU33 4.6 11.7 0.3
C A:GLU33 4.6 11.4 0.7
CB A:PHE26 4.6 11.7 1.0
CG A:ARG27 4.6 20.0 1.0
N A:SER30 4.7 18.1 1.0
CG A:GLU33 4.7 15.0 0.3
CA A:SER30 4.7 18.9 0.8
C A:PHE26 4.7 10.7 1.0
CA A:SER30 4.7 18.6 0.2
CG A:GLU32 4.9 21.1 1.0
O A:HOH741 4.9 57.8 1.0
CG A:GLU33 5.0 16.5 0.7

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 16:49:45 2024

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