Magnesium in PDB 3wkd: 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;

The structure of Crystal Structure of Soluble Epoxide Hydrolase in Complex with Fragment Inhibitor, PDB code: 3wkd 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)	31.08 / 2.48
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.786, 92.786, 245.269, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 26.9

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

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:30.9 occ:1.00 O1 A:PO4602 2.0 52.1 1.0 OD1 A:ASP185 2.1 42.1 1.0 O A:ASP11 2.2 42.4 1.0 OD2 A:ASP9 2.4 35.0 1.0 CG A:ASP185 3.0 36.4 1.0 OD2 A:ASP185 3.1 39.3 1.0 C A:ASP11 3.3 39.0 1.0 CG A:ASP9 3.4 36.4 1.0 P A:PO4602 3.4 38.5 1.0 OD1 A:ASP9 3.7 34.0 1.0 CB A:ASP11 3.9 34.0 1.0 CA A:ASP11 4.0 35.2 1.0 O4 A:PO4602 4.0 39.9 1.0 OD1 A:ASP184 4.1 29.6 1.0 O2 A:PO4602 4.2 38.6 1.0 O3 A:PO4602 4.3 50.0 1.0 CD1 A:ILE186 4.3 41.9 1.0 CB A:ASP185 4.4 32.8 1.0 N A:GLY12 4.4 37.0 1.0 OD2 A:ASP11 4.4 35.2 1.0 N A:ASP11 4.5 31.7 1.0 N A:ASP185 4.6 35.5 1.0 CA A:GLY12 4.6 35.9 1.0 CG A:ASP11 4.7 35.9 1.0 CG1 A:ILE186 4.7 39.1 1.0 CB A:ASP9 4.8 31.0 1.0 CG A:ASP184 4.8 31.0 1.0 OD2 A:ASP184 4.9 28.3 1.0 CA A:ASP185 4.9 36.9 1.0

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