Magnesium in PDB 8bpy: X-Ray Structure of PDE9A in Complex with Inhibitor 13A

All present enzymatic activity of X-Ray Structure of PDE9A in Complex with Inhibitor 13A:
3.1.4.35;

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy was solved by H.Steuber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 3.30
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	222.423, 222.423, 120.257, 90, 90, 90
R / Rfree (%)	24.6 / 31.2

The structure of X-Ray Structure of PDE9A in Complex with Inhibitor 13A also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A (pdb code 8bpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A, PDB code: 8bpy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:13.8 occ:0.00 OD2 A:ASP293 2.0 55.0 1.0 CG A:ASP293 2.5 63.5 1.0 OD1 A:ASP293 2.8 41.9 1.0 NE2 A:HIS325 3.7 92.7 1.0 CB A:ASP293 3.7 67.1 1.0 OE2 A:GLU322 3.9 94.4 1.0 ZN A:ZN2001 3.9 17.1 0.0 CD2 A:HIS292 4.1 83.8 1.0 CA A:ASP293 4.1 76.6 1.0 CD2 A:HIS325 4.1 97.2 1.0 O A:HIS292 4.2 85.2 1.0 O A:THR363 4.2 137.9 1.0 NE2 A:HIS252 4.2 115.2 1.0 OG1 A:THR363 4.2 119.8 1.0 OD1 A:ASP402 4.3 51.7 1.0 CD2 A:HIS296 4.3 105.8 1.0 CD2 A:HIS252 4.4 109.9 1.0 NE2 A:HIS292 4.5 79.3 1.0 NE2 A:HIS296 4.5 106.0 1.0 OD2 A:ASP402 4.6 75.8 1.0 CD A:GLU322 4.6 90.2 1.0 CG A:GLU322 4.7 84.2 1.0 C A:HIS292 4.8 81.1 1.0 N A:ASP293 4.8 82.8 1.0 CE1 A:HIS325 4.8 97.3 1.0 CB A:THR363 4.9 119.8 1.0 CG A:ASP402 4.9 72.2 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of PDE9A in Complex with Inhibitor 13A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of PDE9A in Complex with Inhibitor 13A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:59.8 occ:0.00 OD1 B:ASP293 1.4 113.7 1.0 CG B:ASP293 2.4 136.9 1.0 OG1 B:THR363 2.7 127.2 1.0 OD2 B:ASP293 2.8 126.3 1.0 OE2 B:GLU322 3.0 166.4 1.0 OD2 B:ASP402 3.2 115.5 1.0 CB B:ASP293 3.8 131.9 1.0 O B:THR363 3.9 135.8 1.0 ZN B:ZN2001 3.9 63.1 0.0 NE2 B:HIS252 4.0 121.4 1.0 CB B:THR363 4.1 128.0 1.0 CD B:GLU322 4.1 153.5 1.0 O B:HIS292 4.1 183.5 1.0 NE2 B:HIS325 4.2 126.5 1.0 CD2 B:HIS292 4.2 161.9 1.0 CD2 B:HIS325 4.2 118.1 1.0 CD2 B:HIS296 4.3 128.1 1.0 CG B:ASP402 4.3 126.3 1.0 CA B:ASP293 4.3 131.6 1.0 NE2 B:HIS296 4.4 123.9 1.0 CG B:GLU322 4.4 151.0 1.0 CD2 B:HIS252 4.4 124.7 1.0 OD1 B:ASP402 4.4 82.3 1.0 NE2 B:HIS292 4.5 150.1 1.0 C B:THR363 4.6 130.8 1.0 C B:HIS292 4.8 168.7 1.0 CE1 B:HIS252 4.9 126.5 1.0 N B:ASP293 4.9 136.7 1.0 CG2 B:THR363 5.0 139.5 1.0

D.Meibom, S.Micus, A.L.Andreevski, S.Anlauf, P.Bogner, C.J.Von Buehler, A.P.Dieskau, J.Dreher, F.Eitner, D.Fliegner, M.Follmann, K.M.Gericke, S.Maassen, J.Meyer, K.H.Schlemmer, H.Steuber, A.Tersteegen, F.Wunder. Bay-7081: A Potent, Selective, and Orally Bioavailable Cyanopyridone-Based PDE9A Inhibitor. J.Med.Chem. V. 65 16420 2022.
ISSN: ISSN 0022-2623
PubMed: 36475653
DOI: 10.1021/ACS.JMEDCHEM.2C01267