Atomistry » Magnesium » PDB 4y2r-4y8n » 4y2r
Atomistry »
  Magnesium »
    PDB 4y2r-4y8n »
      4y2r »

Magnesium in PDB 4y2r: Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile

Enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile

All present enzymatic activity of Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile:
3.3.2.10;

Protein crystallography data

The structure of Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile, PDB code: 4y2r 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) 75.96 / 2.45
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.289, 92.289, 244.068, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile (pdb code 4y2r). 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-(Piperazin-1- Yl)Nicotinonitrile, PDB code: 4y2r:

Magnesium binding site 1 out of 1 in 4y2r

Go back to Magnesium Binding Sites List in 4y2r
Magnesium binding site 1 out of 1 in the Structure of Soluble Epoxide Hydrolase in Complex with 2-(Piperazin-1- Yl)Nicotinonitrile


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-(Piperazin-1- Yl)Nicotinonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:38.0
occ:1.00
 OD1 A:ASP185 2.4 27.3 1.0
OD2 A:ASP9 2.7 39.4 1.0
O A:ASP11 2.9 36.4 1.0
CG A:ASP185 3.4 25.6 1.0
OD2 A:ASP185 3.7 26.4 1.0
CG A:ASP9 3.8 34.8 1.0
OD1 A:ASP184 3.9 32.7 1.0
CD1 A:ILE186 3.9 36.3 1.0
C A:ASP11 4.0 33.7 1.0
CB A:ASP11 4.2 32.5 1.0
CG1 A:ILE186 4.3 32.3 1.0
OD1 A:ASP9 4.4 31.1 1.0
CA A:ASP11 4.6 31.9 1.0
CB A:ILE186 4.8 32.8 1.0
OD2 A:ASP11 4.8 38.4 1.0
CB A:ASP185 4.8 24.2 1.0
N A:ASP185 4.9 25.3 1.0
CG A:ASP184 4.9 30.4 1.0
CB A:ASP9 4.9 32.0 1.0
CG A:ASP11 5.0 36.2 1.0
N A:ASP11 5.0 28.7 1.0
N A:GLY12 5.0 33.4 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 03:46:25 2025

Last articles

Mg in 7EBB
Mg in 7E9E
Mg in 7E4Z
Mg in 7E7Q
Mg in 7E5A
Mg in 7E6G
Mg in 7E4Y
Mg in 7E4R
Mg in 7E4Q
Mg in 7E4P
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy