Magnesium 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 / R_free (%)*	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:

Chlorine

(Cl)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 in 6wod

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Magnesium Binding Sites List in 6wod

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg501 b:11.0 occ:1.00	O25	A:IHP504	2.0	12.2	1.0
	O24	A:IHP504	2.0	14.9	1.0
	O	A:HOH629	2.1	11.9	1.0
	O	A:HOH643	2.1	13.9	1.0
	OE1	A:GLU70	2.1	12.5	1.0
	O	A:GLY50	2.1	10.9	1.0
	CD	A:GLU70	3.0	11.9	1.0
	P5	A:IHP504	3.2	14.4	1.0
	P4	A:IHP504	3.2	15.6	1.0
	C	A:GLY50	3.3	10.1	1.0
	OE2	A:GLU70	3.4	11.9	1.0
	O35	A:IHP504	3.5	19.0	1.0
	O14	A:IHP504	3.6	21.1	1.0
	O34	A:IHP504	3.6	19.1	1.0
	CA	A:GLY51	3.7	10.9	1.0
	O15	A:IHP504	3.8	19.1	1.0
	O	A:HOH626	3.9	42.0	1.0
	N	A:GLY51	4.0	10.0	1.0
	OE2	A:GLU66	4.1	19.6	1.0
	NH1	A:ARG20	4.1	11.3	1.0
	O	A:HOH692	4.3	42.1	1.0
	CG	A:GLU70	4.4	12.8	1.0
	O	A:HOH652	4.4	16.2	1.0
	O45	A:IHP504	4.4	13.5	1.0
	O	A:HOH750	4.5	50.1	1.0
	O44	A:IHP504	4.5	20.2	1.0
	N	A:GLY50	4.5	9.9	1.0
	CA	A:GLY50	4.5	10.6	1.0
	O	A:HOH601	4.5	42.2	1.0
	C5	A:IHP504	4.6	21.1	1.0
	C4	A:IHP504	4.7	19.8	1.0
	NH2	A:ARG115	4.7	22.1	1.0
	O	A:HOH620	5.0	36.5	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: Wed Aug 13 19:50:57 2025

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