Magnesium in PDB 4y2x: Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol, PDB code: 4y2x 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)*	80.31 / 2.50
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	92.731, 92.731, 243.251, 90.00, 90.00, 120.00
*R / R_free (%)*	22 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol (pdb code 4y2x). 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- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol, PDB code: 4y2x:

Magnesium binding site 1 out of 1 in 4y2x

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Magnesium Binding Sites List in 4y2x

Magnesium binding site 1 out of 1 in the Structure of Soluble Epoxide Hydrolase in Complex with 2-({[2- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol

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- (Adamantan-1-Yl)Ethyl]Amino}Methyl)Phenol within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:45.0 occ:1.00	OD1	A:ASP185	2.4	29.0	1.0
	OD2	A:ASP9	2.6	36.3	1.0
	O	A:ASP11	2.6	32.9	1.0
	CG	A:ASP185	3.4	32.8	1.0
	OD2	A:ASP185	3.6	36.1	1.0
	OD1	A:ASP184	3.7	36.9	1.0
	C	A:ASP11	3.7	34.6	1.0
	CD1	A:ILE186	3.8	38.0	1.0
	CG	A:ASP9	3.8	32.8	1.0
	CB	A:ASP11	4.0	33.6	1.0
	CA	A:ASP11	4.3	33.7	1.0
	CG1	A:ILE186	4.4	33.6	1.0
	OD1	A:ASP9	4.5	30.3	1.0
	OD2	A:ASP11	4.6	36.5	1.0
	CG	A:ASP184	4.6	34.5	1.0
	N	A:ASP11	4.7	32.5	1.0
	CB	A:ASP185	4.7	32.5	1.0
	N	A:ASP185	4.7	30.6	1.0
	CG	A:ASP11	4.8	32.8	1.0
	CB	A:ASP9	4.8	30.5	1.0
	N	A:GLY12	4.8	33.3	1.0
	OD2	A:ASP184	4.9	35.5	1.0
	CB	A:ILE186	4.9	32.1	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 12 03:46:40 2025

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