Magnesium in PDB 7f0i: Phosphodiesterase-9A in Complex with Inhibitor 4B

All present enzymatic activity of Phosphodiesterase-9A in Complex with Inhibitor 4B:
3.1.4.35;

The structure of Phosphodiesterase-9A in Complex with Inhibitor 4B, PDB code: 7f0i was solved by Y.Wu, Y.Y.Huang, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.53 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.467, 103.467, 268.921, 90, 90, 90
R / Rfree (%)	27.1 / 33.4

The structure of Phosphodiesterase-9A in Complex with Inhibitor 4B also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium atom in the Phosphodiesterase-9A in Complex with Inhibitor 4B (pdb code 7f0i). 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 4B, PDB code: 7f0i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor 4B


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 4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:18.0 occ:1.00 O A:HOH722 2.1 21.8 1.0 O A:HOH709 2.1 20.7 1.0 O A:HOH748 2.3 23.2 1.0 OD1 A:ASP293 2.4 21.4 1.0 O A:HOH708 2.7 18.0 1.0 CG A:ASP293 3.1 23.6 1.0 OD2 A:ASP293 3.2 28.0 1.0 ZN A:ZN601 3.4 55.8 1.0 OE2 A:GLU322 3.5 22.3 1.0 OG1 A:THR363 4.1 17.9 1.0 CD2 A:HIS292 4.1 21.6 1.0 NE2 A:HIS325 4.1 19.4 1.0 CD2 A:HIS296 4.3 23.5 1.0 CD2 A:HIS325 4.3 18.9 1.0 O A:HIS292 4.3 26.5 1.0 CB A:ASP293 4.4 19.6 1.0 CD A:GLU322 4.6 18.8 1.0 CD2 A:HIS252 4.6 20.4 1.0 NE2 A:HIS292 4.6 26.2 1.0 NE2 A:HIS296 4.7 17.1 1.0 OD2 A:ASP402 4.7 24.7 1.0 CA A:ASP293 4.7 17.1 1.0 NE2 A:HIS252 4.8 22.1 1.0 CG A:GLU322 4.9 20.0 1.0 O A:THR363 5.0 29.0 1.0

Magnesium binding site 2 out of 2 in the Phosphodiesterase-9A in Complex with Inhibitor 4B


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 4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:18.7 occ:1.00 O B:HOH724 1.9 23.1 1.0 O B:HOH722 1.9 18.8 1.0 O B:HOH741 2.1 20.3 1.0 O B:HOH721 2.4 17.3 1.0 OD1 B:ASP293 2.5 21.2 1.0 OD2 B:ASP293 3.1 21.3 1.0 CG B:ASP293 3.2 18.6 1.0 ZN B:ZN601 3.3 38.8 1.0 OD2 B:ASP402 4.0 17.3 1.0 O B:HIS292 4.1 17.4 1.0 OE1 B:GLU322 4.2 24.6 1.0 OG1 B:THR363 4.3 22.6 1.0 NE2 B:HIS252 4.4 19.0 1.0 CB B:THR363 4.5 19.7 1.0 OD1 B:ASP402 4.5 19.8 1.0 O B:HOH707 4.6 13.6 1.0 CB B:ASP293 4.6 16.5 1.0 CD2 B:HIS296 4.6 20.6 1.0 CD2 B:HIS252 4.6 17.4 1.0 CD2 B:HIS292 4.7 17.7 1.0 CG B:ASP402 4.7 18.2 1.0 NE2 B:HIS296 4.8 22.6 1.0 NE2 B:HIS325 4.8 17.4 1.0 CG B:GLU322 4.9 29.5 1.0 CD2 B:HIS325 5.0 16.6 1.0

Y.Wu, Q.Wang, M.Y.Jiang, Y.Y.Huang, Z.Zhu, C.Han, Y.J.Tian, B.Zhang, H.B.Luo. Discovery of Potent Phosphodiesterase-9 Inhibitors For the Treatment of Hepatic Fibrosis J.Med.Chem. V. 64 9537 2021.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C00862