Magnesium in PDB 8tfa: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa 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) 36.10 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.304, 59.64, 62.698, 90, 90, 90
R / Rfree (%) 15.4 / 16.9

Other elements in 8tfa:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk (pdb code 8tfa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk, PDB code: 8tfa:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.6
occ:1.00
 O55 A:U6J401 2.0 18.0 1.0
O35 A:U6J401 2.1 18.6 1.0
O44 A:U6J401 2.1 19.7 1.0
OE1 A:GLU70 2.1 18.8 1.0
O A:GLY50 2.1 17.8 1.0
O A:HOH529 2.1 18.9 1.0
CD A:GLU70 3.0 19.0 1.0
MG A:MG403 3.2 18.9 1.0
PA5 A:U6J401 3.2 18.9 1.0
PA4 A:U6J401 3.3 19.8 1.0
OE2 A:GLU70 3.3 18.4 1.0
C A:GLY50 3.3 17.2 1.0
PB5 A:U6J401 3.4 20.3 1.0
O45 A:U6J401 3.5 19.5 1.0
O A:HOH573 3.6 21.1 1.0
O14 A:U6J401 3.6 21.0 1.0
CA A:GLY51 3.7 17.1 1.0
O24 A:U6J401 3.7 20.1 1.0
O15 A:U6J401 3.9 19.4 1.0
N A:GLY51 4.0 17.3 1.0
OE2 A:GLU66 4.0 18.7 1.0
O75 A:U6J401 4.1 23.0 1.0
NH1 A:ARG20 4.1 18.0 1.0
O A:HOH534 4.3 23.3 1.0
N A:GLY50 4.4 17.7 1.0
CG A:GLU70 4.4 18.8 1.0
O65 A:U6J401 4.5 18.8 1.0
CA A:GLY50 4.5 18.0 1.0
O25 A:U6J401 4.5 20.3 1.0
O34 A:U6J401 4.5 23.2 1.0
F A:F406 4.6 22.8 1.0
NH2 A:ARG115 4.7 24.3 1.0
C5 A:U6J401 4.7 22.1 1.0
C4 A:U6J401 4.7 23.5 1.0
CD A:GLU66 4.8 20.4 1.0

Magnesium binding site 2 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:18.9
occ:1.00
 F A:F406 2.0 22.8 1.0
OE2 A:GLU66 2.0 18.7 1.0
O A:HOH560 2.1 19.9 1.0
O55 A:U6J401 2.1 18.0 1.0
O A:HOH573 2.1 21.1 1.0
OE1 A:GLU70 2.1 18.8 1.0
CD A:GLU66 3.1 20.4 1.0
PB5 A:U6J401 3.1 20.3 1.0
CD A:GLU70 3.1 19.0 1.0
MG A:MG402 3.2 18.6 1.0
OE1 A:GLU66 3.5 20.7 1.0
CG A:GLU70 3.5 18.8 1.0
MG A:MG404 3.5 20.2 1.0
O A:HOH504 3.5 23.8 1.0
O65 A:U6J401 3.6 18.8 1.0
O75 A:U6J401 3.7 23.0 1.0
O44 A:U6J401 3.8 19.7 1.0
OE2 A:GLU69 4.0 22.9 1.0
O A:GLY50 4.0 17.8 1.0
O A:HOH670 4.2 33.0 1.0
OE2 A:GLU70 4.3 18.4 1.0
O A:HOH565 4.3 22.4 1.0
O A:HOH542 4.3 25.7 1.0
CG A:GLU66 4.4 18.3 1.0
O A:HOH620 4.5 29.5 1.0
O45 A:U6J401 4.5 19.5 1.0
CA A:GLY51 4.5 17.1 1.0
CB A:GLU66 4.8 18.2 1.0
C A:GLY50 4.8 17.2 1.0
O35 A:U6J401 4.8 18.6 1.0
O A:HOH631 4.9 22.3 1.0
NH2 A:ARG115 4.9 24.3 1.0
O A:HOH529 4.9 18.9 1.0
CB A:GLU70 5.0 17.8 1.0

Magnesium binding site 3 out of 3 in 8tfa

Go back to Magnesium Binding Sites List in 8tfa
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Myo-5-Pp-IP4, Produced Upon Myo-(2OH)-IP5 Phosphorylation By Tvipk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:20.2
occ:1.00
 F A:F406 2.0 22.8 1.0
O65 A:U6J401 2.1 18.8 1.0
OE1 A:GLU66 2.1 20.7 1.0
O A:HOH575 2.1 22.4 1.0
O A:HOH565 2.1 22.4 1.0
O A:HOH631 2.1 22.3 1.0
CD A:GLU66 3.1 20.4 1.0
PB5 A:U6J401 3.1 20.3 1.0
OE2 A:GLU66 3.4 18.7 1.0
MG A:MG403 3.5 18.9 1.0
O A:HOH504 3.7 23.8 1.0
O55 A:U6J401 3.7 18.0 1.0
O75 A:U6J401 3.8 23.0 1.0
NH1 A:ARG65 4.0 20.3 1.0
OE2 A:GLU69 4.0 22.9 1.0
N A:GLY52 4.1 18.0 1.0
O A:HOH584 4.1 27.6 1.0
O A:HOH648 4.1 44.3 1.0
O A:HOH638 4.2 36.0 1.0
O A:HOH502 4.3 41.2 1.0
O A:HOH560 4.3 19.9 1.0
O A:GLY52 4.3 20.0 1.0
CG A:GLU66 4.4 18.3 1.0
O45 A:U6J401 4.5 19.5 1.0
O A:HOH670 4.5 33.0 1.0
O A:HOH573 4.7 21.1 1.0
CA A:GLY51 4.8 17.1 1.0
CA A:GLY52 4.8 18.8 1.0
C A:GLY51 4.8 18.0 1.0
NH2 A:ARG65 4.9 20.4 1.0
CZ A:ARG65 4.9 19.2 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: Fri Oct 4 20:36:59 2024

Last articles

Fe in 9CUF
Fe in 9DEU
Fe in 9CCB
Fe in 9D86
Fe in 9DCO
Fe in 9EBM
Fe in 9EBK
Fe in 8ZQD
Fe in 8ZEH
Fe in 8ZET
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy