Magnesium in PDB 4y2q: Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine, PDB code: 4y2q was solved by Y.Amano, T.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	76.13 / 2.40
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	92.544, 92.544, 243.634, 90.00, 90.00, 120.00
*R / R_free (%)*	19.6 / 25.7

Other elements in 4y2q:

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine (pdb code 4y2q). 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 Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine, PDB code: 4y2q:

Magnesium binding site 1 out of 1 in 4y2q

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Magnesium Binding Sites List in 4y2q

Magnesium binding site 1 out of 1 in the Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Soluble Epoxide Hydrolase in Complex with 1-[3- (Trifluoromethyl)Pyridin-2-Yl]Piperazine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:46.3 occ:1.00	OD1	A:ASP185	2.3	32.5	1.0
	OD2	A:ASP9	2.5	43.4	1.0
	O	A:ASP11	2.8	38.6	1.0
	CG	A:ASP185	3.3	29.2	1.0
	OD2	A:ASP185	3.5	31.5	1.0
	CG	A:ASP9	3.6	38.0	1.0
	CD1	A:ILE186	3.7	46.4	1.0
	C	A:ASP11	3.8	37.0	1.0
	OD1	A:ASP184	3.9	30.9	1.0
	CB	A:ASP11	4.0	36.0	1.0
	OD1	A:ASP9	4.2	35.4	1.0
	CA	A:ASP11	4.4	34.4	1.0
	CG1	A:ILE186	4.5	38.5	1.0
	CB	A:ASP185	4.6	28.2	1.0
	N	A:ASP185	4.7	28.1	1.0
	CB	A:ASP9	4.8	33.8	1.0
	N	A:ASP11	4.8	30.8	1.0
	CG	A:ASP184	4.8	33.2	1.0
	N	A:GLY12	4.9	35.7	1.0
	OD2	A:ASP11	4.9	36.1	1.0
	CB	A:ILE186	4.9	40.1	1.0
	CG	A:ASP11	5.0	37.6	1.0

Reference:

Y.Amano, E.Tanabe, T.Yamaguchi. Identification of N-Ethylmethylamine As A Novel Scaffold For Inhibitors of Soluble Epoxide Hydrolase By Crystallographic Fragment Screening Bioorg.Med.Chem. V. 23 2310 2015.
ISSN: ESSN 1464-3391
PubMed: 25862210
DOI: 10.1016/J.BMC.2015.03.083

Page generated: Tue Aug 20 16:24:13 2024

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