Magnesium in PDB 3jsi: Human Phosphodiesterase 9 in Complex with Inhibitor

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

The structure of Human Phosphodiesterase 9 in Complex with Inhibitor, PDB code: 3jsi was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.65 / 2.72
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.099, 104.099, 271.040, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 21.8

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

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Human Phosphodiesterase 9 in Complex with Inhibitor (pdb code 3jsi). 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 Inhibitor, PDB code: 3jsi:
Jump to Magnesium binding site number: 1; 2;

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:76.9 occ:1.00 O A:HOH954 2.0 42.6 1.0 O A:HOH953 2.0 55.2 1.0 O A:HOH951 2.1 48.0 1.0 O A:HOH952 2.2 41.4 1.0 OD1 A:ASP293 2.3 45.0 1.0 CG A:ASP293 3.3 44.3 1.0 OD2 A:ASP293 3.6 49.4 1.0 ZN A:ZN901 3.7 79.2 1.0 OE2 A:GLU322 3.9 43.8 1.0 OG1 A:THR363 4.2 35.0 1.0 NE2 A:HIS325 4.2 38.3 1.0 O A:HIS292 4.3 37.5 1.0 CD2 A:HIS325 4.4 38.2 1.0 CD2 A:HIS292 4.4 40.0 1.0 CD2 A:HIS296 4.5 41.0 1.0 NE2 A:HIS252 4.5 41.0 1.0 OD2 A:ASP402 4.6 59.6 1.0 CB A:ASP293 4.7 34.9 1.0 NE2 A:HIS296 4.7 41.1 1.0 CD2 A:HIS252 4.7 41.1 1.0 CD A:GLU322 4.8 51.6 1.0 CB A:THR363 4.8 36.1 1.0 NE2 A:HIS292 4.9 39.9 1.0 OD1 A:ASP402 5.0 53.9 1.0 CG A:GLU322 5.0 40.0 1.0

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


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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:44.6 occ:1.00 O B:HOH959 1.9 29.0 1.0 O B:HOH956 2.0 37.4 1.0 OD1 B:ASP293 2.3 44.9 1.0 O B:HOH958 2.4 66.3 1.0 O B:HOH957 3.0 53.0 1.0 CG B:ASP293 3.3 45.7 1.0 O B:HOH965 3.6 32.8 1.0 OD2 B:ASP293 3.6 52.8 1.0 ZN B:ZN901 3.7 77.1 1.0 OE2 B:GLU322 3.9 54.9 1.0 OG1 B:THR363 4.2 44.0 1.0 NE2 B:HIS325 4.2 39.4 1.0 O B:HIS292 4.3 42.9 1.0 CD2 B:HIS325 4.4 39.5 1.0 CD2 B:HIS292 4.4 46.2 1.0 CD2 B:HIS296 4.4 45.1 1.0 NE2 B:HIS252 4.5 43.3 1.0 OD2 B:ASP402 4.6 62.5 1.0 NE2 B:HIS296 4.6 45.0 1.0 CB B:ASP293 4.7 38.8 1.0 CD2 B:HIS252 4.7 43.7 1.0 CB B:THR363 4.8 43.8 1.0 CD B:GLU322 4.8 55.5 1.0 NE2 B:HIS292 5.0 46.3 1.0 OD1 B:ASP402 5.0 55.4 1.0

P.R.Verhoest, C.Proulx-Lafrance, M.Corman, L.Chenard, C.J.Helal, X.Hou, R.Kleiman, S.Liu, E.Marr, F.S.Menniti, C.J.Schmidt, M.Vanase-Frawley, A.W.Schmidt, R.D.Williams, F.R.Nelson, K.R.Fonseca, S.Liras. Identification of A Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement As A Rapid Lead Optimization Strategy. J.Med.Chem. V. 52 7946 2009.
ISSN: ISSN 0022-2623
PubMed: 19919087
DOI: 10.1021/JM9015334