Zinc in PDB 4qge: Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D

The structure of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D, PDB code: 4qge was solved by Y.-X.Shao, M.Huang, W.Cui, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.580, 103.580, 268.657, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 26.8

The structure of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D (pdb code 4qge). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D, PDB code: 4qge:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:38.1 occ:1.00 OD2 A:ASP293 2.1 28.1 1.0 OD1 A:ASP402 2.1 30.7 1.0 NE2 A:HIS256 2.1 29.5 1.0 NE2 A:HIS292 2.1 26.1 1.0 O A:HOH702 2.4 27.1 1.0 O A:HOH701 2.5 26.6 1.0 CD2 A:HIS292 3.0 21.9 1.0 CE1 A:HIS256 3.1 22.3 1.0 CG A:ASP402 3.1 28.0 1.0 CD2 A:HIS256 3.1 22.2 1.0 CG A:ASP293 3.1 25.0 1.0 CE1 A:HIS292 3.2 24.1 1.0 OD2 A:ASP402 3.5 30.1 1.0 OD1 A:ASP293 3.7 23.8 1.0 MG A:MG603 3.8 28.0 1.0 O A:HOH745 4.1 26.4 1.0 CD2 A:HIS252 4.1 23.1 1.0 CG A:HIS292 4.2 23.8 1.0 ND1 A:HIS256 4.2 24.1 1.0 ND1 A:HIS292 4.2 22.4 1.0 CG A:HIS256 4.2 24.3 1.0 CB A:ASP293 4.3 23.5 1.0 O A:HOH704 4.3 28.7 1.0 NE2 A:HIS252 4.4 23.1 1.0 CB A:ASP402 4.4 27.8 1.0 O A:ASP402 4.6 26.9 1.0 O A:HOH705 4.8 16.8 1.0 CG2 A:VAL260 4.8 20.1 1.0 CA A:ASP402 4.8 27.6 1.0

Zinc binding site 2 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:41.9 occ:1.00 OD2 B:ASP293 2.0 30.7 1.0 OD1 B:ASP402 2.1 30.1 1.0 NE2 B:HIS292 2.1 31.6 1.0 NE2 B:HIS256 2.1 31.4 1.0 O B:HOH701 2.3 34.9 1.0 O B:HOH702 2.4 23.8 1.0 CD2 B:HIS292 2.9 26.9 1.0 CE1 B:HIS256 3.1 27.0 1.0 CG B:ASP402 3.1 26.7 1.0 CD2 B:HIS256 3.1 25.6 1.0 CG B:ASP293 3.2 28.3 1.0 CE1 B:HIS292 3.2 29.2 1.0 OD2 B:ASP402 3.5 31.2 1.0 OD1 B:ASP293 3.7 29.9 1.0 MG B:MG603 3.8 29.0 1.0 CD2 B:HIS252 4.1 24.3 1.0 CG B:HIS292 4.1 26.9 1.0 O B:HOH716 4.2 31.5 1.0 ND1 B:HIS256 4.2 27.8 1.0 ND1 B:HIS292 4.2 27.8 1.0 CG B:HIS256 4.2 27.2 1.0 CB B:ASP293 4.3 23.6 1.0 NE2 B:HIS252 4.3 23.1 1.0 O B:HOH704 4.3 31.1 1.0 CB B:ASP402 4.4 26.8 1.0 O B:HOH773 4.5 44.3 1.0 O B:ASP402 4.6 25.1 1.0 O B:HOH703 4.7 18.4 1.0 CG2 B:VAL260 4.8 26.3 1.0 CA B:ASP402 4.8 26.0 1.0

Y.X.Shao, M.Huang, W.Cui, L.J.Feng, Y.Wu, Y.Cai, Z.Li, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Discovery of A Phosphodiesterase-9A Inhibitor As A Potential Hypoglycemic Agent. J.Med.Chem. 2014.
ISSN: ISSN 0022-2623
PubMed: 25432025
DOI: 10.1021/JM500836H