Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Phosphodiesterase-9A in Complex with Inhibitor Wyq-C36D, PDB code: 4qge:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:28.0 occ:1.00 OD1 A:ASP293 2.1 23.8 1.0 O A:HOH702 2.3 27.1 1.0 O A:HOH704 2.3 28.7 1.0 O A:HOH706 2.3 17.8 1.0 O A:HOH705 2.4 16.8 1.0 O A:HOH703 2.5 22.4 1.0 CG A:ASP293 3.1 25.0 1.0 OD2 A:ASP293 3.3 28.1 1.0 ZN A:ZN602 3.8 38.1 1.0 OE2 A:GLU322 4.0 27.8 1.0 NE2 A:HIS325 4.0 19.2 1.0 CD2 A:HIS296 4.1 23.7 1.0 O A:HOH701 4.1 26.6 1.0 O A:HIS292 4.2 24.6 1.0 O A:HOH707 4.3 37.2 1.0 CD2 A:HIS325 4.3 17.3 1.0 CD2 A:HIS292 4.3 21.9 1.0 CB A:ASP293 4.4 23.5 1.0 OG1 A:THR363 4.4 23.3 1.0 CD2 A:HIS252 4.4 23.1 1.0 NE2 A:HIS252 4.5 23.1 1.0 NE2 A:HIS296 4.6 25.7 1.0 NE2 A:HIS292 4.7 26.1 1.0 CA A:ASP293 4.7 22.6 1.0 OD2 A:ASP402 4.8 30.1 1.0 O A:HOH752 4.9 35.7 1.0 CD A:GLU322 4.9 26.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:29.0 occ:1.00 OD1 B:ASP293 2.1 29.9 1.0 O B:HOH706 2.3 18.8 1.0 O B:HOH705 2.3 18.5 1.0 O B:HOH701 2.3 34.9 1.0 O B:HOH703 2.3 18.4 1.0 O B:HOH704 2.3 31.1 1.0 CG B:ASP293 3.0 28.3 1.0 OD2 B:ASP293 3.3 30.7 1.0 ZN B:ZN602 3.8 41.9 1.0 O B:HOH773 3.8 44.3 1.0 OE2 B:GLU322 3.9 27.1 1.0 NE2 B:HIS325 4.0 20.2 1.0 O B:HOH702 4.1 23.8 1.0 OG1 B:THR363 4.2 21.4 1.0 CD2 B:HIS292 4.2 26.9 1.0 CD2 B:HIS325 4.2 20.0 1.0 O B:HOH711 4.3 19.2 1.0 CD2 B:HIS296 4.3 22.2 1.0 O B:HIS292 4.3 25.1 1.0 CB B:ASP293 4.4 23.6 1.0 NE2 B:HIS252 4.5 23.1 1.0 CD2 B:HIS252 4.6 24.3 1.0 NE2 B:HIS292 4.6 31.6 1.0 O B:HOH755 4.7 33.9 1.0 OD2 B:ASP402 4.7 31.2 1.0 NE2 B:HIS296 4.7 23.8 1.0 O B:THR363 4.7 24.7 1.0 CA B:ASP293 4.8 22.9 1.0 CB B:THR363 4.8 23.1 1.0 O B:HOH720 4.9 27.5 1.0 CD B:GLU322 4.9 28.4 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