Magnesium in PDB 8t99: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion, PDB code: 8t99 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) 31.45 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.824, 59.634, 62.653, 90, 90, 90
R / Rfree (%) 15.6 / 18.3

Other elements in 8t99:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion (pdb code 8t99). 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-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion, PDB code: 8t99:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8t99

Go back to Magnesium Binding Sites List in 8t99
Magnesium binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:13.5
occ:1.00
 O22 A:ZOW401 2.0 13.0 1.0
O51 A:ZOW401 2.1 13.2 1.0
O31 A:ZOW401 2.1 13.0 1.0
OE1 A:GLU70 2.1 13.5 1.0
O A:GLY50 2.1 11.3 1.0
O A:HOH552 2.1 13.4 1.0
CD A:GLU70 3.0 13.6 1.0
MG A:MG403 3.2 12.7 1.0
PA1 A:ZOW401 3.2 13.6 1.0
C A:GLY50 3.3 11.0 1.0
OE2 A:GLU70 3.3 12.9 1.0
PA2 A:ZOW401 3.3 15.4 1.0
PB1 A:ZOW401 3.4 14.7 1.0
O41 A:ZOW401 3.5 14.9 1.0
O A:HOH576 3.6 13.8 1.0
O12 A:ZOW401 3.6 16.9 1.0
CA A:GLY51 3.7 11.2 1.0
O32 A:ZOW401 3.8 14.3 1.0
N A:GLY51 3.9 11.4 1.0
OE2 A:GLU66 3.9 12.1 1.0
O11 A:ZOW401 4.0 14.0 1.0
O71 A:ZOW401 4.1 15.1 1.0
NH1 A:ARG20 4.1 12.3 1.0
N A:GLY50 4.4 11.7 1.0
CG A:GLU70 4.4 13.0 1.0
CA A:GLY50 4.4 12.4 1.0
O61 A:ZOW401 4.5 13.6 1.0
O A:HOH551 4.5 19.7 1.0
O21 A:ZOW401 4.5 14.9 1.0
O42 A:ZOW401 4.5 18.4 1.0
NH2 A:ARG115 4.6 17.5 1.0
C2 A:ZOW401 4.7 17.4 1.0
F A:F407 4.7 17.3 1.0
C1 A:ZOW401 4.7 17.1 1.0
CD A:GLU66 4.8 13.3 1.0
O A:HOH540 4.9 28.3 1.0

Magnesium binding site 2 out of 3 in 8t99

Go back to Magnesium Binding Sites List in 8t99
Magnesium binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:12.7
occ:1.00
 OE2 A:GLU66 2.0 12.1 1.0
F A:F407 2.0 17.3 1.0
O51 A:ZOW401 2.0 13.2 1.0
O A:HOH561 2.1 15.6 1.0
O A:HOH576 2.1 13.8 1.0
OE1 A:GLU70 2.1 13.5 1.0
CD A:GLU66 3.1 13.3 1.0
PB1 A:ZOW401 3.1 14.7 1.0
CD A:GLU70 3.2 13.6 1.0
MG A:MG402 3.2 13.5 1.0
OE1 A:GLU66 3.4 14.3 1.0
O A:HOH502 3.5 17.3 1.0
MG A:MG404 3.5 15.5 1.0
CG A:GLU70 3.5 13.0 1.0
O61 A:ZOW401 3.6 13.6 1.0
O71 A:ZOW401 3.6 15.1 1.0
O22 A:ZOW401 3.7 13.0 1.0
OE2 A:GLU69 4.0 16.5 1.0
O A:GLY50 4.0 11.3 1.0
OE2 A:GLU70 4.3 12.9 1.0
O A:HOH683 4.3 28.1 1.0
O A:HOH564 4.3 16.7 1.0
O A:HOH536 4.4 18.9 1.0
CG A:GLU66 4.4 12.2 1.0
O41 A:ZOW401 4.5 14.9 1.0
CA A:GLY51 4.5 11.2 1.0
O A:HOH628 4.5 21.8 1.0
C A:GLY50 4.7 11.0 1.0
CB A:GLU66 4.8 12.7 1.0
O31 A:ZOW401 4.8 13.0 1.0
NH2 A:ARG115 4.8 17.5 1.0
O A:HOH648 4.9 15.8 1.0
O A:HOH552 4.9 13.4 1.0
N A:GLY51 5.0 11.4 1.0

Magnesium binding site 3 out of 3 in 8t99

Go back to Magnesium Binding Sites List in 8t99
Magnesium binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with Scyllo-L-1,4-[Pp]2-(2,3)IP2, 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-L-1,4-[Pp]2-(2,3)IP2, Mg, and Fluoride Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:15.5
occ:1.00
 F A:F407 2.0 17.3 1.0
OE1 A:GLU66 2.1 14.3 1.0
O61 A:ZOW401 2.1 13.6 1.0
O A:HOH564 2.1 16.7 1.0
O A:HOH584 2.1 16.3 1.0
O A:HOH648 2.1 15.8 1.0
CD A:GLU66 3.1 13.3 1.0
PB1 A:ZOW401 3.1 14.7 1.0
OE2 A:GLU66 3.4 12.1 1.0
MG A:MG403 3.5 12.7 1.0
O51 A:ZOW401 3.6 13.2 1.0
O71 A:ZOW401 3.8 15.1 1.0
O A:HOH502 3.8 17.3 1.0
NH1 A:ARG65 4.0 15.0 1.0
OE2 A:GLU69 4.0 16.5 1.0
N A:GLY52 4.1 12.5 1.0
O A:HOH609 4.1 22.6 1.0
O A:HOH681 4.2 28.9 1.0
O A:HOH509 4.2 34.6 1.0
O A:HOH561 4.3 15.6 1.0
O A:HOH664 4.4 33.6 1.0
O A:GLY52 4.4 13.6 1.0
CG A:GLU66 4.4 12.2 1.0
O A:HOH636 4.4 43.2 1.0
O41 A:ZOW401 4.5 14.9 1.0
O A:HOH545 4.6 49.5 1.0
O A:HOH576 4.7 13.8 1.0
CA A:GLY51 4.7 11.2 1.0
O A:HOH683 4.8 28.1 1.0
CA A:GLY52 4.8 12.7 1.0
C A:GLY51 4.8 12.2 1.0
NH2 A:ARG65 4.9 13.6 1.0
CZ A:ARG65 5.0 13.7 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 20:34:11 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy