Magnesium in PDB 6fl8: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp:
2.7.1.158;

Protein crystallography data

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp, PDB code: 6fl8 was solved by H.L.Whitfield, C.A.Brearley, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	54.30 / 2.10
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	59.990, 61.450, 83.430, 89.55, 88.00, 62.08
*R / R_free (%)*	19.8 / 24.7

Other elements in 6fl8:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp (pdb code 6fl8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp, PDB code: 6fl8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6fl8

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Magnesium Binding Sites List in 6fl8

Magnesium binding site 1 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg503 b:53.8 occ:1.00	O1B	A:ADP502	2.2	44.4	1.0
	O1A	A:ADP502	2.3	45.6	1.0
	OD2	A:ASP407	2.3	45.5	1.0
	O	A:HOH698	2.3	51.3	1.0
	O	A:HOH697	2.4	58.7	1.0
	O	A:HOH678	3.1	40.1	1.0
	CG	A:ASP407	3.3	46.2	1.0
	PB	A:ADP502	3.5	48.0	1.0
	PA	A:ADP502	3.5	42.6	1.0
	O3A	A:ADP502	3.7	38.6	1.0
	HO14	A:TIY501	3.8	71.1	0.9
	CB	A:ASP407	4.0	37.8	1.0
	H5'2	A:ADP502	4.1	48.8	1.0
	O3B	A:ADP502	4.1	44.7	1.0
	OD1	A:ASP407	4.3	44.9	1.0
	O2A	A:ADP502	4.6	41.5	1.0
	O14	A:TIY501	4.6	59.3	0.9
	O5'	A:ADP502	4.6	40.3	1.0
	O2B	A:ADP502	4.7	40.3	1.0
	CA	A:GLY19	4.8	46.1	1.0
	H3'	A:ADP502	4.8	44.4	1.0
	O	A:HOH710	4.8	51.9	1.0
	O3'	A:ADP502	4.9	41.6	1.0
	HO16	A:TIY501	4.9	69.9	0.9
	C5'	A:ADP502	4.9	40.6	1.0
	HO3'	A:ADP502	4.9	50.0	1.0

Magnesium binding site 2 out of 3 in 6fl8

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Magnesium Binding Sites List in 6fl8

Magnesium binding site 2 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg503 b:68.5 occ:1.00	OD1	B:ASP407	2.8	50.2	1.0
	O2B	B:ADP502	3.0	45.7	0.9
	OG	B:SER409	3.2	45.8	1.0
	OD2	B:ASP407	3.4	50.8	1.0
	CG	B:ASP407	3.5	48.9	1.0
	PB	B:ADP502	3.9	41.7	0.9
	O3B	B:ADP502	4.0	44.0	0.9
	CB	B:ALA21	4.1	45.6	1.0
	CB	B:SER409	4.3	40.4	1.0
	NZ	B:LYS411	4.5	36.0	1.0
	O1B	B:ADP502	4.6	45.1	0.9
	NH2	B:ARG40	4.7	37.4	1.0
	MG	B:MG504	4.9	49.4	1.0
	N	B:ALA21	5.0	50.8	1.0
	CB	B:ASP407	5.0	40.7	1.0

Magnesium binding site 3 out of 3 in 6fl8

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Magnesium Binding Sites List in 6fl8

Magnesium binding site 3 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Purpurogallin and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg504 b:49.4 occ:1.00	OD2	B:ASP407	2.1	50.8	1.0
	O2A	B:ADP502	2.3	43.2	0.9
	O	B:HOH672	2.3	48.1	1.0
	O3B	B:ADP502	2.4	44.0	0.9
	O	B:HOH654	2.5	46.8	1.0
	O	B:HOH647	2.8	43.0	1.0
	CG	B:ASP407	3.2	48.9	1.0
	PA	B:ADP502	3.7	40.6	0.9
	CB	B:ASP407	3.7	40.7	1.0
	PB	B:ADP502	3.7	41.7	0.9
	H5'2	B:ADP502	4.0	42.4	0.9
	O3A	B:ADP502	4.1	39.1	0.9
	OD1	B:ASP407	4.3	50.2	1.0
	O2B	B:ADP502	4.3	45.7	0.9
	H3'	B:ADP502	4.6	46.6	0.9
	O5'	B:ADP502	4.7	35.9	0.9
	O1A	B:ADP502	4.7	41.2	0.9
	O3'	B:ADP502	4.7	36.8	0.9
	HO3'	B:ADP502	4.7	44.2	0.9
	OG	B:SER370	4.7	39.3	1.0
	C5'	B:ADP502	4.9	35.3	0.9
	O	B:ASP368	4.9	35.2	1.0
	MG	B:MG503	4.9	68.5	1.0
	O1B	B:ADP502	4.9	45.1	0.9

Reference:

H.Whitfield, M.Gilmartin, K.Baker, A.M.Riley, H.Y.Godage, B.V.L.Potter, A.M.Hemmings, C.A.Brearley. A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase. J. Med. Chem. V. 61 8838 2018.
ISSN: ISSN 1520-4804
PubMed: 30160967
DOI: 10.1021/ACS.JMEDCHEM.8B01022

Page generated: Wed Aug 13 06:08:44 2025

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