Magnesium in PDB 6cyd: PDE2 in Complex with Compound 7

All present enzymatic activity of PDE2 in Complex with Compound 7:
3.1.4.17;

The structure of PDE2 in Complex with Compound 7, PDB code: 6cyd was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.91 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.940, 91.820, 102.830, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21

The structure of PDE2 in Complex with Compound 7 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the PDE2 in Complex with Compound 7 (pdb code 6cyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PDE2 in Complex with Compound 7, PDB code: 6cyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PDE2 in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE2 in Complex with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:16.2 occ:1.00 O A:HOH1106 2.0 14.1 1.0 O A:HOH1101 2.0 14.6 1.0 O A:HOH1175 2.0 17.0 1.0 OD1 A:ASP697 2.0 15.2 1.0 O A:HOH1223 2.1 18.1 1.0 O A:HOH1138 2.1 16.0 1.0 CG A:ASP697 3.1 14.2 1.0 OD2 A:ASP697 3.5 12.8 1.0 ZN A:ZN1001 4.0 19.7 1.0 O A:HOH1218 4.0 16.5 1.0 OG1 A:THR768 4.1 15.8 1.0 NE2 A:HIS730 4.1 15.8 1.0 OE2 A:GLU727 4.1 18.1 1.0 O A:HOH1238 4.1 17.5 1.0 CD2 A:HIS730 4.3 16.0 1.0 O A:HIS696 4.3 15.4 1.0 CD2 A:HIS696 4.3 15.2 1.0 CB A:ASP697 4.4 12.3 1.0 OD2 A:ASP808 4.5 16.7 1.0 O A:THR768 4.5 15.4 1.0 CD2 A:HIS700 4.5 15.4 1.0 NE2 A:HIS656 4.5 16.4 1.0 CB A:THR768 4.6 18.5 1.0 CD2 A:HIS656 4.7 16.9 1.0 NE2 A:HIS700 4.7 15.4 1.0 NE2 A:HIS696 4.7 14.8 1.0 CA A:ASP697 4.8 11.1 1.0 O A:HOH1131 4.8 40.2 1.0 CG A:GLU727 4.8 17.5 1.0 CD A:GLU727 4.9 23.1 1.0

Magnesium binding site 2 out of 2 in the PDE2 in Complex with Compound 7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE2 in Complex with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:18.3 occ:1.00 O B:HOH1239 2.1 15.1 1.0 OD1 B:ASP697 2.1 15.7 1.0 O B:HOH1103 2.1 16.7 1.0 O B:HOH1113 2.1 13.7 1.0 O B:HOH1102 2.1 16.3 1.0 O B:HOH1135 2.2 17.6 1.0 CG B:ASP697 3.1 15.0 1.0 OD2 B:ASP697 3.5 15.6 1.0 NE2 B:HIS730 4.0 15.4 1.0 ZN B:ZN1001 4.0 20.8 1.0 O B:HOH1186 4.1 16.6 1.0 OG1 B:THR768 4.1 16.7 1.0 O B:HOH1119 4.2 20.1 1.0 OE2 B:GLU727 4.2 24.1 1.0 CD2 B:HIS730 4.3 15.6 1.0 O B:HIS696 4.3 14.9 1.0 CD2 B:HIS696 4.3 15.6 1.0 CB B:ASP697 4.4 13.2 1.0 O B:HOH1176 4.5 29.1 1.0 CD2 B:HIS700 4.5 15.1 1.0 OD2 B:ASP808 4.5 18.5 1.0 NE2 B:HIS656 4.6 18.3 1.0 CB B:THR768 4.6 16.6 1.0 O2 B:EDO1004 4.6 44.0 1.0 O B:THR768 4.7 17.5 1.0 CD2 B:HIS656 4.8 18.1 1.0 NE2 B:HIS700 4.8 14.8 1.0 CA B:ASP697 4.8 12.9 1.0 NE2 B:HIS696 4.8 15.7 1.0 CG B:GLU727 4.9 16.2 1.0 CD B:GLU727 5.0 23.2 1.0

S.J.Stachel, R.Berger, A.B.Nomland, A.T.Ginnetti, D.V.Paone, D.Wang, V.Puri, H.Lange, J.Drott, J.Lu, J.Marcus, M.P.Dwyer, S.Suon, J.M.Uslaner, S.M.Smith. Structure-Guided Design and Procognitive Assessment of A Potent and Selective Phosphodiesterase 2A Inhibitor. Acs Med Chem Lett V. 9 815 2018.
ISSN: ISSN 1948-5875
PubMed: 30128073
DOI: 10.1021/ACSMEDCHEMLETT.8B00214