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: Sat Apr 3 14:08:02 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy