Magnesium in PDB 3i8v: Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone

All present enzymatic activity of Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone:
3.1.4.17;

The structure of Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone, PDB code: 3i8v was solved by R.K.Y.Cheng, L.Crawley, J.Barker, M.Wood, B.Felicetti, M.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.33 / 2.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.406, 105.406, 165.252, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.2

The structure of Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone (pdb code 3i8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone, PDB code: 3i8v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone


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 Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg623 b:26.2 occ:1.00 O A:HOH114 2.1 23.8 1.0 OD1 A:ASP413 2.1 26.9 1.0 O A:HOH174 2.1 28.1 1.0 O A:HOH151 2.1 21.6 1.0 O A:HOH64 2.1 20.7 1.0 O A:HOH6 2.3 22.9 1.0 CG A:ASP413 3.1 25.9 1.0 OD2 A:ASP413 3.4 27.9 1.0 ZN A:ZN2 3.8 31.4 1.0 OE2 A:GLU442 3.9 29.4 1.0 OG1 A:THR483 4.0 28.3 1.0 O A:HOH634 4.1 26.1 1.0 O A:HIS412 4.2 24.1 1.0 CD2 A:HIS412 4.2 24.6 1.0 O3 A:0MO1 4.3 55.7 1.0 O A:HOH636 4.3 29.8 1.0 NE2 A:HIS445 4.3 24.9 1.0 O A:THR483 4.4 28.8 1.0 CB A:ASP413 4.5 25.0 1.0 CD2 A:HIS445 4.5 23.4 1.0 NE2 A:HIS412 4.6 27.8 1.0 CB A:THR483 4.6 28.2 1.0 CD2 A:HIS416 4.7 25.2 1.0 OD2 A:ASP530 4.7 35.6 1.0 NE2 A:HIS372 4.8 29.2 1.0 CD A:GLU442 4.8 28.9 1.0 CG A:GLU442 4.8 27.6 1.0 CA A:ASP413 4.8 25.0 1.0 CD2 A:HIS372 4.9 27.1 1.0 O A:HOH105 4.9 26.7 1.0 C A:HIS412 5.0 24.6 1.0 NE2 A:HIS416 5.0 27.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg623 b:24.7 occ:1.00 OD1 B:ASP413 2.0 24.4 1.0 O B:HOH74 2.1 24.1 1.0 O B:HOH60 2.1 25.6 1.0 O B:HOH162 2.1 23.6 1.0 O B:HOH69 2.2 21.7 1.0 O B:HOH38 2.2 23.3 1.0 CG B:ASP413 3.1 26.1 1.0 OD2 B:ASP413 3.4 28.1 1.0 ZN B:ZN1 3.7 33.6 1.0 OE2 B:GLU442 4.0 25.7 1.0 O3 B:0MO2 4.1 56.3 1.0 OG1 B:THR483 4.1 26.8 1.0 O B:HIS412 4.1 25.7 1.0 NE2 B:HIS445 4.2 22.9 1.0 CD2 B:HIS412 4.2 24.7 1.0 O B:HOH636 4.3 24.2 1.0 O B:HOH158 4.4 26.9 1.0 CD2 B:HIS445 4.4 23.4 1.0 CB B:ASP413 4.4 25.5 1.0 CD2 B:HIS416 4.5 22.7 1.0 NE2 B:HIS412 4.5 25.8 1.0 O B:THR483 4.5 29.0 1.0 NE2 B:HIS372 4.6 28.2 1.0 OD2 B:ASP530 4.7 34.2 1.0 CB B:THR483 4.7 28.1 1.0 O B:HOH637 4.7 39.8 1.0 CD2 B:HIS372 4.8 27.9 1.0 NE2 B:HIS416 4.8 25.2 1.0 CA B:ASP413 4.8 25.6 1.0 O B:HOH155 4.8 34.3 1.0 CD B:GLU442 4.9 26.7 1.0 C14 B:0MO2 4.9 55.8 1.0 CG B:GLU442 4.9 25.0 1.0 C B:HIS412 4.9 25.9 1.0

R.K.Y.Cheng, L.Crawley, J.Barker, M.Wood, B.Felicetti, M.Whittaker. Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone To Be Published.