Magnesium in PDB 4y2y: Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine, PDB code: 4y2y 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)*	80.26 / 2.30
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	92.673, 92.673, 243.751, 90.00, 90.00, 120.00
*R / R_free (%)*	20.3 / 26.5

Other elements in 4y2y:

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine also contains other interesting chemical elements:

Fluorine

(F)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine (pdb code 4y2y). 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 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine, PDB code: 4y2y:

Magnesium binding site 1 out of 1 in 4y2y

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Magnesium Binding Sites List in 4y2y

Magnesium binding site 1 out of 1 in the Structure of Soluble Epoxide Hydrolase in Complex with 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine

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 2-(2- Fluorophenyl)-N-[(5-Methyl-2-Thienyl)Methyl]Ethanamine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:46.9 occ:1.00	OD1	A:ASP185	2.4	30.2	1.0
	OD2	A:ASP9	2.8	40.2	1.0
	O	A:ASP11	2.9	39.8	1.0
	CG	A:ASP185	3.4	28.6	1.0
	OD2	A:ASP185	3.6	31.6	1.0
	OD1	A:ASP184	3.8	40.5	1.0
	CD1	A:ILE186	3.8	46.8	1.0
	C	A:ASP11	3.9	37.5	1.0
	CG	A:ASP9	4.0	37.6	1.0
	CG1	A:ILE186	4.2	40.1	1.0
	CB	A:ASP11	4.2	36.5	1.0
	OD2	A:ASP11	4.4	41.6	1.0
	CA	A:ASP11	4.6	35.5	1.0
	OD1	A:ASP9	4.6	36.3	1.0
	CB	A:ASP185	4.7	28.8	1.0
	CB	A:ILE186	4.7	39.3	1.0
	N	A:ASP185	4.8	30.0	1.0
	CG	A:ASP184	4.8	35.8	1.0
	CG	A:ASP11	4.9	36.4	1.0
	N	A:ILE186	4.9	35.4	1.0
	N	A:GLY12	4.9	37.3	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 16:24:31 2024

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