Zinc 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
Magnesium	(Mg)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human PDE4A with 4-(3-Butoxy-4-Methoxyphenyl) Methyl-2-Imidazolidone, PDB code: 3i8v:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn2 b:31.4 occ:1.00 OD2 A:ASP413 2.1 27.9 1.0 NE2 A:HIS376 2.2 28.5 1.0 NE2 A:HIS412 2.2 27.8 1.0 OD1 A:ASP530 2.2 29.6 1.0 O A:HOH114 2.3 23.8 1.0 O A:HOH634 2.3 26.1 1.0 CD2 A:HIS412 3.1 24.6 1.0 CE1 A:HIS376 3.1 30.0 1.0 CG A:ASP413 3.2 25.9 1.0 CG A:ASP530 3.2 30.7 1.0 CD2 A:HIS376 3.2 29.0 1.0 CE1 A:HIS412 3.2 25.2 1.0 OD2 A:ASP530 3.5 35.6 1.0 OD1 A:ASP413 3.6 26.9 1.0 MG A:MG623 3.8 26.2 1.0 O A:HOH6 4.0 22.9 1.0 O A:HOH625 4.1 29.1 1.0 CD2 A:HIS372 4.1 27.1 1.0 ND1 A:HIS376 4.3 28.7 1.0 CG A:HIS412 4.3 25.9 1.0 ND1 A:HIS412 4.3 25.9 1.0 CG A:HIS376 4.3 28.5 1.0 NE2 A:HIS372 4.3 29.2 1.0 CB A:ASP413 4.4 25.0 1.0 CB A:ASP530 4.5 29.5 1.0 O A:HOH174 4.7 28.1 1.0 CG2 A:VAL380 4.8 25.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn1 b:33.6 occ:1.00 OD2 B:ASP413 2.1 28.1 1.0 OD1 B:ASP530 2.1 28.0 1.0 NE2 B:HIS376 2.2 24.4 1.0 NE2 B:HIS412 2.2 25.8 1.0 O B:HOH74 2.3 24.1 1.0 O B:HOH636 2.4 24.2 1.0 CG B:ASP530 3.1 30.4 1.0 CD2 B:HIS412 3.1 24.7 1.0 CD2 B:HIS376 3.1 24.7 1.0 CG B:ASP413 3.1 26.1 1.0 CE1 B:HIS376 3.2 25.6 1.0 CE1 B:HIS412 3.2 26.3 1.0 OD2 B:ASP530 3.4 34.2 1.0 OD1 B:ASP413 3.6 24.4 1.0 MG B:MG623 3.7 24.7 1.0 O B:HOH60 3.9 25.6 1.0 O B:HOH11 4.1 29.7 1.0 CD2 B:HIS372 4.1 27.9 1.0 NE2 B:HIS372 4.2 28.2 1.0 CG B:HIS412 4.3 26.5 1.0 ND1 B:HIS412 4.3 26.7 1.0 CG B:HIS376 4.3 26.0 1.0 ND1 B:HIS376 4.3 25.2 1.0 CB B:ASP413 4.4 25.5 1.0 CB B:ASP530 4.5 28.1 1.0 O B:HOH162 4.7 23.6 1.0 CG2 B:VAL380 4.7 29.7 1.0 O3 B:0MO2 4.8 56.3 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.