Atomistry » Chlorine » PDB 6wjy-6wup » 6woe
Atomistry »
  Chlorine »
    PDB 6wjy-6wup »
      6woe »

Chlorine in PDB 6woe: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN 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 10MIN 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 10MIN 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 10MIN in the Absence of Fluoride., PDB code: 6woe 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) 31.60 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.265, 59.639, 62.693, 90, 90, 90
R / Rfree (%) 12.7 / 15.2

Other elements in 6woe:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Inositol Hexakisphosphate and Mg, Presoaked with 5-IP7, Mg and Fluoride, Soaking 10MIN 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 10MIN in the Absence of Fluoride. (pdb code 6woe). 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 10MIN in the Absence of Fluoride., PDB code: 6woe:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6woe

Go back to Chlorine Binding Sites List in 6woe
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 10MIN 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 10MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:14.5
occ:1.00
 O A:HOH692 2.9 34.1 1.0
O A:HOH629 3.1 12.5 1.0
O A:HOH712 3.2 15.4 1.0
ND2 A:ASN86 3.3 18.0 1.0
CE1 A:HIS91 3.7 12.7 1.0
NE2 A:GLN136 3.7 14.1 1.0
CG A:GLN136 3.8 10.1 1.0
CB A:VAL135 4.0 11.4 1.0
CB A:ASN86 4.1 12.7 1.0
CG A:ASN86 4.2 14.3 1.0
CD A:LYS133 4.2 13.3 0.5
CD A:GLN136 4.2 10.7 1.0
CD A:LYS133 4.3 13.9 0.5
NE2 A:HIS91 4.4 14.2 1.0
O A:HOH660 4.4 47.9 1.0
N A:GLN136 4.5 9.6 1.0
CG1 A:VAL135 4.5 11.8 1.0
CG2 A:VAL135 4.7 12.9 1.0
OH A:TYR139 4.7 10.2 1.0
NZ A:LYS133 4.7 18.1 0.5
O A:HOH657 4.8 12.0 1.0
ND1 A:HIS91 4.8 11.2 1.0
CE A:LYS133 4.8 14.8 0.5
CA A:VAL135 4.9 11.1 1.0
CB A:GLN136 5.0 10.3 1.0
C A:VAL135 5.0 10.2 1.0

Chlorine binding site 2 out of 2 in 6woe

Go back to Chlorine Binding Sites List in 6woe
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 10MIN 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 10MIN in the Absence of Fluoride. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:16.8
occ:1.00
 O A:HOH658 3.0 33.2 1.0
OG A:SER28 3.1 17.9 1.0
N A:GLU32 3.1 15.1 1.0
OG A:SER30 3.2 23.5 0.4
N A:SER28 3.3 13.1 1.0
N A:GLU33 3.3 13.5 0.5
N A:GLU33 3.3 13.1 0.5
CB A:ARG27 3.6 16.6 1.0
N A:GLU31 3.7 16.3 1.0
O A:SER28 3.7 14.7 1.0
N A:ARG27 3.8 11.2 1.0
O A:GLU33 3.8 11.8 0.5
O A:GLU33 3.8 11.6 0.5
CB A:SER28 3.9 17.4 1.0
CA A:GLU32 3.9 15.9 1.0
CA A:SER28 3.9 15.4 1.0
CA A:GLU31 4.0 15.8 1.0
CB A:GLU32 4.0 19.1 1.0
C A:GLU31 4.0 15.7 1.0
CA A:ARG27 4.0 13.2 1.0
C A:ARG27 4.1 12.8 1.0
C A:GLU32 4.1 13.7 1.0
C A:SER28 4.1 16.1 1.0
CA A:GLU33 4.2 12.8 0.5
CA A:GLU33 4.2 12.2 0.5
CB A:GLU33 4.2 15.0 0.5
CB A:GLU33 4.3 14.1 0.5
C A:SER30 4.4 17.8 1.0
CB A:SER30 4.4 19.9 0.6
CB A:SER30 4.5 20.9 0.4
C A:GLU33 4.5 10.9 0.5
C A:GLU33 4.5 10.4 0.5
CB A:PHE26 4.6 12.1 1.0
CG A:GLU33 4.6 17.7 0.5
N A:SER30 4.7 19.1 1.0
C A:PHE26 4.7 10.5 1.0
CA A:SER30 4.7 20.3 0.6
CA A:SER30 4.7 20.3 0.4
CG A:ARG27 4.7 21.9 1.0
O A:HOH753 4.8 39.6 1.0
CG A:GLU32 4.9 23.5 1.0
CA A:PHE26 5.0 10.9 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 16:49:42 2024

Last articles

Ca in 5TD4
Ca in 5TF9
Ca in 5TAK
Ca in 5TAE
Ca in 5TAJ
Ca in 5TAI
Ca in 5T9T
Ca in 5TAD
Ca in 5T5O
Ca in 5TA5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy