Magnesium in PDB 6fjk: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 and Adp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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 Myo-IP6 and Adp, PDB code: 6fjk 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)*	83.95 / 2.03
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	59.810, 60.340, 83.980, 88.53, 89.18, 63.36
*R / R_free (%)*	17.8 / 22.5

Other elements in 6fjk:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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 Myo-IP6 and Adp (pdb code 6fjk). 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 Myo-IP6 and Adp, PDB code: 6fjk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6fjk

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Magnesium Binding Sites List in 6fjk

Magnesium binding site 1 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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 Myo-IP6 and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg503 b:58.6 occ:1.00	O22	A:I6P501	2.4	58.4	1.0
	OD1	A:ASP407	2.8	62.6	1.0
	O1B	A:ADP502	2.8	87.7	1.0
	O3B	A:ADP502	3.0	83.7	1.0
	PB	A:ADP502	3.2	68.4	1.0
	O33	A:I6P501	3.2	32.5	1.0
	OD2	A:ASP407	3.3	72.9	1.0
	CG	A:ASP407	3.4	60.6	1.0
	O2B	A:ADP502	3.7	56.1	1.0
	CB	A:ALA21	3.8	34.1	1.0
	P2	A:I6P501	3.8	51.7	1.0
	OG	A:SER409	3.9	48.1	1.0
	O43	A:I6P501	3.9	31.4	1.0
	P3	A:I6P501	4.0	30.5	1.0
	ND2	A:ASN22	4.2	31.7	1.0
	CB	A:SER409	4.2	35.8	1.0
	O32	A:I6P501	4.3	63.7	1.0
	O	A:HOH628	4.4	43.7	1.0
	O13	A:I6P501	4.4	19.8	1.0
	NH2	A:ARG40	4.4	37.8	1.0
	N	A:ALA21	4.4	22.8	1.0
	OD2	A:ASP368	4.4	39.1	1.0
	NZ	A:LYS411	4.5	15.7	1.0
	O42	A:I6P501	4.7	42.3	1.0
	CA	A:ALA21	4.7	31.8	1.0
	O3A	A:ADP502	4.7	79.0	1.0
	O12	A:I6P501	4.8	25.8	1.0
	CB	A:ASP407	4.9	35.8	1.0

Magnesium binding site 2 out of 3 in 6fjk

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Magnesium Binding Sites List in 6fjk

Magnesium binding site 2 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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 Myo-IP6 and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg503 b:48.7 occ:1.00	O32	B:I6P501	2.4	60.7	1.0
	OD1	B:ASP407	2.7	71.6	1.0
	O1B	B:ADP502	2.8	0.9	1.0
	OD2	B:ASP407	3.1	71.2	1.0
	O2B	B:ADP502	3.2	0.8	1.0
	CG	B:ASP407	3.2	65.6	1.0
	O33	B:I6P501	3.3	36.6	1.0
	PB	B:ADP502	3.3	97.5	1.0
	P2	B:I6P501	3.5	57.3	1.0
	O22	B:I6P501	3.5	69.5	1.0
	O3B	B:ADP502	4.0	96.0	1.0
	CB	B:ALA21	4.0	35.7	1.0
	OG	B:SER409	4.1	50.1	1.0
	ND2	B:ASN22	4.2	36.2	1.0
	O43	B:I6P501	4.2	38.0	1.0
	P3	B:I6P501	4.2	31.0	1.0
	OD2	B:ASP368	4.2	33.1	1.0
	NZ	B:LYS411	4.3	23.9	1.0
	O13	B:I6P501	4.4	25.8	1.0
	O12	B:I6P501	4.5	28.0	1.0
	N	B:ALA21	4.5	31.6	1.0
	NH2	B:ARG40	4.5	49.6	1.0
	CB	B:SER409	4.5	37.7	1.0
	O42	B:I6P501	4.6	65.9	1.0
	CB	B:ASP407	4.7	44.5	1.0
	O3A	B:ADP502	4.8	88.7	1.0
	CA	B:ALA21	4.9	35.7	1.0

Magnesium binding site 3 out of 3 in 6fjk

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Magnesium Binding Sites List in 6fjk

Magnesium binding site 3 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Myo-IP6 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 Myo-IP6 and Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg504 b:46.8 occ:1.00	OD2	B:ASP407	2.6	71.2	1.0
	OG	B:SER370	2.9	34.4	1.0
	O	B:ASP368	2.9	26.0	1.0
	O	B:HOH606	3.4	44.0	1.0
	CG	B:ASP407	3.4	65.6	1.0
	CB	B:ASP407	3.5	44.5	1.0
	C	B:CYS369	3.5	26.3	1.0
	N	B:SER370	3.6	20.5	1.0
	CB	B:SER370	3.7	29.3	1.0
	O	B:CYS369	3.9	25.1	1.0
	CA	B:CYS369	3.9	24.0	1.0
	O2A	B:ADP502	3.9	68.5	1.0
	C	B:ASP368	4.0	26.6	1.0
	CE	B:LYS168	4.0	33.4	1.0
	O32	B:I6P501	4.1	60.7	1.0
	CD	B:LYS168	4.1	23.2	1.0
	O42	B:I6P501	4.1	65.9	1.0
	CA	B:SER370	4.2	26.8	1.0
	CG	B:LYS168	4.3	22.4	1.0
	O	B:HOH733	4.3	51.0	1.0
	N	B:CYS369	4.4	20.5	1.0
	OD1	B:ASP407	4.6	71.6	1.0
	NZ	B:LYS168	4.7	34.4	1.0
	O	B:ILE406	4.7	25.1	1.0
	P2	B:I6P501	4.7	57.3	1.0
	O	B:ASP407	4.8	31.7	1.0
	CB	B:LYS168	4.9	30.8	1.0
	O2B	B:ADP502	4.9	0.8	1.0
	CA	B:ASP407	4.9	35.2	1.0
	OE2	B:GLU166	5.0	38.9	1.0
	OD2	B:ASP368	5.0	33.1	1.0

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: Tue Oct 1 00:29:58 2024

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