Magnesium in PDB 3wk9: Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor

Enzymatic activity of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor

All present enzymatic activity of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor:
3.1.3.76; 3.3.2.10;

Protein crystallography data

The structure of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor, PDB code: 3wk9 was solved by Y.Amano, T.Yamaguchi, E.Tanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.05 / 2.20
*Space group*	P 6₅ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	92.489, 92.489, 245.217, 90.00, 90.00, 120.00
*R / R_free (%)*	20.3 / 25.2

Other elements in 3wk9:

The structure of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor also contains other interesting chemical elements:

Bromine

(Br)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor (pdb code 3wk9). 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 Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor, PDB code: 3wk9:

Magnesium binding site 1 out of 1 in 3wk9

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Magnesium Binding Sites List in 3wk9

Magnesium binding site 1 out of 1 in the Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:41.2 occ:1.00	O1	A:PO4602	2.0	43.1	1.0
	OD2	A:ASP9	2.1	37.4	1.0
	O	A:ASP11	2.2	41.2	1.0
	OD1	A:ASP185	2.3	31.8	1.0
	CG	A:ASP185	3.1	33.8	1.0
	CG	A:ASP9	3.1	40.0	1.0
	OD2	A:ASP185	3.2	36.4	1.0
	C	A:ASP11	3.2	38.8	1.0
	OD1	A:ASP9	3.5	36.0	1.0
	P	A:PO4602	3.5	38.8	1.0
	CB	A:ASP11	3.8	35.6	1.0
	CA	A:ASP11	3.9	36.8	1.0
	OD1	A:ASP184	4.0	35.4	1.0
	OD2	A:ASP11	4.2	39.5	1.0
	O4	A:PO4602	4.3	46.2	1.0
	N	A:ASP11	4.3	36.1	1.0
	O2	A:PO4602	4.3	40.6	1.0
	O3	A:PO4602	4.3	45.1	1.0
	N	A:GLY12	4.3	37.4	1.0
	N	A:ASP185	4.5	34.5	1.0
	CB	A:ASP9	4.5	29.7	1.0
	CB	A:ASP185	4.5	34.2	1.0
	CG	A:ASP11	4.5	38.5	1.0
	CG	A:ASP184	4.6	34.9	1.0
	CA	A:GLY12	4.6	40.1	1.0
	OD2	A:ASP184	4.7	36.2	1.0
	CD1	A:ILE186	4.8	42.9	1.0
	CG1	A:ILE186	4.8	42.0	1.0
	CA	A:ASP185	5.0	36.1	1.0

Reference:

Y.Amano, T.Yamaguchi, E.Tanabe. Structural Insights Into Binding of Inhibitors to Soluble Epoxide Hydrolase Gained By Fragment Screening and X-Ray Crystallography Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 24656800
DOI: 10.1016/J.BMC.2014.03.001

Page generated: Mon Aug 11 04:54:22 2025

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