Magnesium in PDB 6gfh: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp:
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 Neo-IP5 and Atp, PDB code: 6gfh 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)*	29.34 / 2.65
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	59.632, 60.563, 84.482, 87.81, 88.43, 63.01
*R / R_free (%)*	19.9 / 26.8

Other elements in 6gfh:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp 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 Neo-IP5 and Atp (pdb code 6gfh). 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 Neo-IP5 and Atp, PDB code: 6gfh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6gfh

Go back to

Magnesium Binding Sites List in 6gfh

Magnesium binding site 1 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

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 Neo-IP5 and Atp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg503 b:44.9 occ:1.00	OD2	A:ASP407	2.0	43.9	1.0
	O1B	A:ATP502	2.3	53.4	1.0
	CG	A:ASP407	2.6	44.5	1.0
	OD1	A:ASP407	2.6	49.5	1.0
	O33	A:K7V501	3.4	48.6	0.9
	O1G	A:ATP502	3.5	57.8	1.0
	PB	A:ATP502	3.6	49.1	1.0
	O23	A:K7V501	3.8	52.0	0.9
	NZ	A:LYS411	3.9	45.2	1.0
	CB	A:ASP407	4.1	36.1	1.0
	P3	A:K7V501	4.1	59.6	0.9
	PG	A:ATP502	4.2	72.3	1.0
	O3B	A:ATP502	4.2	50.5	1.0
	CB	A:SER409	4.3	49.8	1.0
	O3G	A:ATP502	4.3	51.5	1.0
	O2B	A:ATP502	4.4	45.0	1.0
	CB	A:ALA21	4.4	39.3	1.0
	OG	A:SER409	4.5	55.7	1.0
	O13	A:K7V501	4.6	55.2	0.9
	O12	A:K7V501	4.6	52.6	0.9
	NH2	A:ARG40	4.7	40.9	1.0
	O3A	A:ATP502	4.9	50.5	1.0
	H2	A:K7V501	4.9	64.6	0.9
	ND2	A:ASN22	4.9	44.0	1.0

Magnesium binding site 2 out of 3 in 6gfh

Go back to

Magnesium Binding Sites List in 6gfh

Magnesium binding site 2 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

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 Neo-IP5 and Atp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg503 b:44.5 occ:1.00	O1G	B:ATP502	2.2	47.6	1.0
	O2G	B:ATP502	2.5	58.5	1.0
	PG	B:ATP502	2.8	68.3	1.0
	OG	B:SER370	3.0	50.1	1.0
	O	B:ASP368	3.0	36.5	1.0
	O2A	B:ATP502	3.1	48.4	1.0
	CB	B:ASP407	3.3	44.3	1.0
	OD1	B:ASP407	3.3	53.4	1.0
	CG	B:ASP407	3.4	47.0	1.0
	O3G	B:ATP502	3.9	57.7	1.0
	O3B	B:ATP502	4.0	52.4	1.0
	C	B:CYS369	4.2	39.6	1.0
	N	B:SER370	4.2	39.4	1.0
	C	B:ASP368	4.2	35.2	1.0
	OD2	B:ASP407	4.2	52.2	1.0
	CA	B:CYS369	4.3	39.9	1.0
	OD2	B:ASP368	4.3	52.3	1.0
	CB	B:SER370	4.4	44.8	1.0
	CD	B:LYS168	4.4	38.4	1.0
	CE	B:LYS168	4.5	38.3	1.0
	PA	B:ATP502	4.6	44.1	1.0
	NZ	B:LYS168	4.6	43.7	1.0
	O	B:CYS369	4.6	36.8	1.0
	CA	B:ASP407	4.7	40.2	1.0
	N	B:CYS369	4.8	31.6	1.0
	CG	B:ASP368	4.8	49.3	1.0
	CG	B:LYS168	4.8	37.4	1.0
	HO3'	B:ATP502	4.8	60.4	1.0
	O	B:ASP407	4.8	46.8	1.0
	OE2	B:GLU166	4.9	51.5	1.0
	O2B	B:ATP502	4.9	47.9	1.0
	CA	B:SER370	4.9	42.1	1.0
	O5'	B:ATP502	4.9	52.0	1.0

Magnesium binding site 3 out of 3 in 6gfh

Go back to

Magnesium Binding Sites List in 6gfh

Magnesium binding site 3 out of 3 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From A. Thaliana in Complex with Neo-IP5 and Atp

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 Neo-IP5 and Atp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg504 b:45.8 occ:1.00	OD2	B:ASP407	2.3	52.2	1.0
	O2B	B:ATP502	2.5	47.9	1.0
	OD1	B:ASP407	2.9	53.4	1.0
	OG	B:SER409	2.9	54.5	1.0
	CG	B:ASP407	2.9	47.0	1.0
	O2G	B:ATP502	3.2	58.5	1.0
	CB	B:SER409	3.4	49.1	1.0
	O43	B:K7V501	3.5	52.0	1.0
	OD2	B:ASP368	3.6	52.3	1.0
	PB	B:ATP502	3.9	44.6	1.0
	ND2	B:ASN22	4.4	45.8	1.0
	CB	B:ASP407	4.4	44.3	1.0
	PG	B:ATP502	4.4	68.3	1.0
	CB	B:ALA21	4.5	45.1	1.0
	O23	B:K7V501	4.5	39.3	1.0
	P3	B:K7V501	4.6	50.1	1.0
	O3B	B:ATP502	4.7	52.4	1.0
	CA	B:SER409	4.7	46.3	1.0
	N	B:SER409	4.7	43.1	1.0
	NH2	B:ARG40	4.7	45.4	1.0
	NZ	B:LYS411	4.7	35.2	1.0
	O1B	B:ATP502	4.8	43.5	1.0
	CG	B:ASP368	4.8	49.3	1.0
	O2A	B:ATP502	4.8	48.4	1.0
	O3G	B:ATP502	4.8	57.7	1.0
	O	B:ASP407	4.9	46.8	1.0
	O3A	B:ATP502	4.9	44.0	1.0
	O13	B:K7V501	4.9	49.0	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 01:07:50 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