Magnesium in PDB 4e90: Human Phosphodiesterase 9 in Complex with Inhibitors

All present enzymatic activity of Human Phosphodiesterase 9 in Complex with Inhibitors:
3.1.4.35;

The structure of Human Phosphodiesterase 9 in Complex with Inhibitors, PDB code: 4e90 was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.00 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.579, 103.579, 270.214, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.6

The structure of Human Phosphodiesterase 9 in Complex with Inhibitors also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Human Phosphodiesterase 9 in Complex with Inhibitors (pdb code 4e90). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Phosphodiesterase 9 in Complex with Inhibitors, PDB code: 4e90:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphodiesterase 9 in Complex with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:32.7 occ:1.00 O A:HOH1168 2.1 30.2 1.0 O A:HOH1004 2.3 23.0 1.0 O A:HOH1115 2.4 32.1 1.0 OD1 A:ASP293 2.4 26.2 1.0 O A:HOH1041 2.5 24.7 1.0 CG A:ASP293 3.3 25.8 1.0 OD2 A:ASP293 3.6 32.1 1.0 ZN A:ZN901 3.6 44.9 1.0 OE2 A:GLU322 4.1 23.9 1.0 OG1 A:THR363 4.1 24.8 1.0 O A:HOH1137 4.1 28.1 1.0 CD2 A:HIS292 4.2 28.5 1.0 NE2 A:HIS325 4.2 24.0 1.0 O A:HIS292 4.3 25.8 1.0 OD2 A:ASP402 4.3 29.3 1.0 CD2 A:HIS325 4.4 23.8 1.0 O A:HOH1034 4.5 23.5 1.0 CD2 A:HIS296 4.6 25.7 1.0 CB A:ASP293 4.7 23.2 1.0 NE2 A:HIS252 4.7 26.8 1.0 CB A:THR363 4.7 24.8 1.0 NE2 A:HIS292 4.7 28.6 1.0 O A:THR363 4.7 27.3 1.0 CD2 A:HIS252 4.7 27.0 1.0 CG A:GLU322 4.9 21.4 1.0 CD A:GLU322 4.9 29.6 1.0 OD1 A:ASP402 4.9 33.8 1.0 NE2 A:HIS296 5.0 25.7 1.0 CA A:ASP293 5.0 21.8 1.0

Magnesium binding site 2 out of 2 in the Human Phosphodiesterase 9 in Complex with Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphodiesterase 9 in Complex with Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:38.7 occ:1.00 OD1 B:ASP293 2.2 27.8 1.0 O B:HOH1018 2.4 24.8 1.0 O B:HOH1048 2.4 24.0 1.0 O B:HOH1028 2.6 25.7 1.0 CG B:ASP293 3.2 27.6 1.0 OD2 B:ASP293 3.6 32.1 1.0 ZN B:ZN901 3.8 47.4 1.0 NE2 B:HIS325 4.0 24.1 1.0 OE2 B:GLU322 4.0 36.0 1.0 O B:HIS292 4.0 31.2 1.0 OG1 B:THR363 4.0 26.9 1.0 CD2 B:HIS325 4.1 24.1 1.0 CD2 B:HIS292 4.2 28.9 1.0 O B:HOH1065 4.4 32.8 1.0 O B:HOH1019 4.5 21.1 1.0 OD2 B:ASP402 4.5 34.8 1.0 CB B:ASP293 4.5 25.1 1.0 CD2 B:HIS296 4.5 26.9 1.0 CB B:THR363 4.7 25.1 1.0 CA B:ASP293 4.7 23.8 1.0 NE2 B:HIS292 4.7 29.2 1.0 CG B:GLU322 4.8 27.1 1.0 O B:THR363 4.8 27.3 1.0 CD B:GLU322 4.8 40.8 1.0 C B:HIS292 4.8 29.0 1.0 CD2 B:HIS252 4.8 30.5 1.0 NE2 B:HIS252 4.9 30.4 1.0 NE2 B:HIS296 5.0 26.6 1.0

M.M.Claffey, C.J.Helal, P.R.Verhoest, Z.Kang, K.S.Fors, S.Jung, J.Zhong, M.W.Bundesmann, X.Hou, S.Lui, R.J.Kleiman, M.Vanase-Frawley, A.W.Schmidt, F.Menniti, C.J.Schmidt, W.E.Hoffman, M.Hajos, L.Mcdowell, R.E.O'connor, M.Macdougall-Murphy, K.R.Fonseca, S.L.Becker, F.R.Nelson, S.Liras. Application of Structure-Based Drug Design and Parallel Chemistry to Identify Selective, Brain Penetrant, in Vivo Active Phosphodiesterase 9A Inhibitors. J.Med.Chem. V. 55 9055 2012.
ISSN: ISSN 0022-2623
PubMed: 23025719
DOI: 10.1021/JM3009635