Magnesium in PDB 8t98: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98 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) 36.49 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.103, 59.571, 62.43, 90, 90, 90
R / Rfree (%) 14.9 / 17.2

Other elements in 8t98:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion (pdb code 8t98). 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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion, PDB code: 8t98:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion


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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:10.2
occ:1.00
 O55 A:U6J401 2.0 10.9 1.0
O35 A:U6J401 2.0 10.9 1.0
O24 A:U6J401 2.1 10.9 1.0
OE1 A:GLU70 2.1 10.8 1.0
O A:HOH532 2.1 11.0 1.0
O A:GLY50 2.1 9.6 1.0
CD A:GLU70 3.1 10.9 1.0
MG A:MG403 3.2 11.2 1.0
PA5 A:U6J401 3.2 11.0 1.0
PA4 A:U6J401 3.2 11.8 1.0
OE2 A:GLU70 3.3 10.3 1.0
C A:GLY50 3.3 9.5 1.0
PB5 A:U6J401 3.3 11.1 1.0
O45 A:U6J401 3.5 11.0 1.0
O A:HOH581 3.6 12.6 1.0
O14 A:U6J401 3.6 12.3 1.0
CA A:GLY51 3.7 9.8 1.0
O44 A:U6J401 3.7 12.0 1.0
O15 A:U6J401 3.9 11.9 1.0
OE2 A:GLU66 3.9 11.2 1.0
N A:GLY51 4.0 9.5 1.0
O75 A:U6J401 4.1 12.5 1.0
NH1 A:ARG20 4.2 10.4 1.0
O65 A:U6J401 4.4 11.1 1.0
N A:GLY50 4.4 10.1 1.0
CG A:GLU70 4.4 10.7 1.0
CA A:GLY50 4.5 10.1 1.0
O25 A:U6J401 4.5 11.9 1.0
O A:HOH552 4.5 18.0 1.0
O34 A:U6J401 4.5 14.0 1.0
NH2 A:ARG115 4.6 14.9 1.0
O A:HOH566 4.6 23.2 1.0
F A:F407 4.6 12.5 1.0
C5 A:U6J401 4.7 12.3 1.0
C4 A:U6J401 4.7 12.7 1.0
CD A:GLU66 4.8 12.3 1.0

Magnesium binding site 2 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion


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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.2
occ:1.00
 F A:F407 1.9 12.5 1.0
O A:HOH563 2.0 12.3 1.0
OE2 A:GLU66 2.1 11.2 1.0
O55 A:U6J401 2.1 10.9 1.0
OE1 A:GLU70 2.1 10.8 1.0
O A:HOH581 2.2 12.6 1.0
CD A:GLU66 3.1 12.3 1.0
PB5 A:U6J401 3.1 11.1 1.0
CD A:GLU70 3.2 10.9 1.0
MG A:MG402 3.2 10.2 1.0
OE1 A:GLU66 3.5 12.1 1.0
MG A:MG404 3.5 12.5 1.0
CG A:GLU70 3.5 10.7 1.0
O A:HOH504 3.5 11.9 1.0
O65 A:U6J401 3.6 11.1 1.0
O75 A:U6J401 3.7 12.5 1.0
O24 A:U6J401 3.7 10.9 1.0
OE2 A:GLU69 3.9 15.2 1.0
O A:GLY50 4.0 9.6 1.0
O A:HOH699 4.3 25.4 1.0
OE2 A:GLU70 4.3 10.3 1.0
O A:HOH580 4.3 13.7 1.0
O A:HOH551 4.4 16.9 1.0
CG A:GLU66 4.4 10.6 1.0
O A:HOH651 4.4 18.6 1.0
O45 A:U6J401 4.5 11.0 1.0
CA A:GLY51 4.5 9.8 1.0
CB A:GLU66 4.8 11.2 1.0
C A:GLY50 4.8 9.5 1.0
O35 A:U6J401 4.8 10.9 1.0
NH2 A:ARG115 4.9 14.9 1.0
O A:HOH659 4.9 15.1 1.0
O A:HOH532 4.9 11.0 1.0
CB A:GLU70 5.0 10.2 1.0

Magnesium binding site 3 out of 3 in 8t98

Go back to Magnesium Binding Sites List in 8t98
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion


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 Scyllo-3-Pp-(1,2,4,5)IP4, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.5
occ:1.00
 F A:F407 2.0 12.5 1.0
OE1 A:GLU66 2.1 12.1 1.0
O A:HOH583 2.1 14.2 1.0
O65 A:U6J401 2.1 11.1 1.0
O A:HOH659 2.1 15.1 1.0
O A:HOH580 2.1 13.7 1.0
CD A:GLU66 3.1 12.3 1.0
PB5 A:U6J401 3.2 11.1 1.0
OE2 A:GLU66 3.5 11.2 1.0
MG A:MG403 3.5 11.2 1.0
O55 A:U6J401 3.7 10.9 1.0
O A:HOH504 3.7 11.9 1.0
O75 A:U6J401 3.7 12.5 1.0
OE2 A:GLU69 4.0 15.2 1.0
NH1 A:ARG65 4.0 12.9 1.0
N A:GLY52 4.1 10.8 1.0
O A:HOH594 4.1 17.9 1.0
O A:HOH531 4.1 26.8 1.0
O A:HOH536 4.3 27.0 1.0
O A:HOH505 4.3 28.4 1.0
O A:GLY52 4.3 11.7 1.0
O A:HOH563 4.4 12.3 1.0
O A:HOH668 4.4 36.5 1.0
CG A:GLU66 4.4 10.6 1.0
O45 A:U6J401 4.5 11.0 1.0
O A:HOH648 4.6 35.6 1.0
O A:HOH699 4.7 25.4 1.0
O A:HOH581 4.7 12.6 1.0
CA A:GLY51 4.7 9.8 1.0
CA A:GLY52 4.8 11.4 1.0
C A:GLY51 4.8 10.0 1.0
NH2 A:ARG65 4.9 13.0 1.0
CZ A:ARG65 4.9 12.4 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 20:33:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy