Magnesium in PDB 6cyb: 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: 6cyb was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.17 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.260, 96.640, 102.040, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.1

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

Fluorine	(F)	12 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the PDE2 in Complex with Compound 7 (pdb code 6cyb). 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: 6cyb:
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:14.7 occ:1.00 O A:HOH1120 2.0 14.6 1.0 OD1 A:ASP697 2.1 14.2 1.0 O A:HOH1103 2.1 14.1 1.0 O A:HOH1101 2.1 13.8 1.0 O A:HOH1220 2.1 13.5 1.0 O A:HOH1137 2.2 14.1 1.0 CG A:ASP697 3.1 14.4 1.0 OD2 A:ASP697 3.5 14.3 1.0 OE2 A:GLU727 4.1 18.7 1.0 NE2 A:HIS730 4.1 13.7 1.0 ZN A:ZN1001 4.1 18.2 1.0 O A:HOH1202 4.1 13.8 1.0 OG1 A:THR768 4.1 17.0 1.0 O A:HOH1232 4.2 16.1 1.0 CD2 A:HIS696 4.3 14.4 1.0 CD2 A:HIS730 4.3 14.0 1.0 O A:HIS696 4.3 13.2 1.0 CB A:ASP697 4.4 12.1 1.0 CD2 A:HIS700 4.5 14.5 1.0 CB A:THR768 4.5 19.3 1.0 OD2 A:ASP808 4.5 17.3 1.0 O A:THR768 4.6 15.4 1.0 NE2 A:HIS656 4.6 15.7 1.0 O A:HOH1133 4.7 31.9 1.0 NE2 A:HIS696 4.7 13.6 1.0 NE2 A:HIS700 4.7 14.4 1.0 CA A:ASP697 4.8 12.4 1.0 CD2 A:HIS656 4.8 15.4 1.0 CG A:GLU727 4.8 15.6 1.0 CD A:GLU727 4.9 18.5 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:16.0 occ:1.00 O B:HOH1104 2.1 14.3 1.0 OD1 B:ASP697 2.1 15.1 1.0 O B:HOH1114 2.1 14.8 1.0 O B:HOH1101 2.1 14.6 1.0 O B:HOH1246 2.1 14.9 1.0 O B:HOH1157 2.2 14.9 1.0 CG B:ASP697 3.1 14.1 1.0 OD2 B:ASP697 3.5 13.8 1.0 O B:HOH1192 4.0 15.2 1.0 NE2 B:HIS730 4.1 14.9 1.0 ZN B:ZN1001 4.1 18.5 1.0 OG1 B:THR768 4.1 15.7 1.0 O B:HOH1225 4.1 17.6 1.0 OE2 B:GLU727 4.2 20.3 1.0 O B:HIS696 4.3 14.0 1.0 CD2 B:HIS696 4.3 14.2 1.0 CD2 B:HIS730 4.3 15.1 1.0 CB B:ASP697 4.5 12.7 1.0 CD2 B:HIS700 4.5 16.5 1.0 OD2 B:ASP808 4.5 16.8 1.0 CB B:THR768 4.5 16.0 1.0 NE2 B:HIS656 4.6 14.8 1.0 O B:THR768 4.6 17.1 1.0 O B:HOH1141 4.6 26.7 1.0 NE2 B:HIS696 4.7 13.1 1.0 NE2 B:HIS700 4.7 16.5 1.0 CA B:ASP697 4.8 12.5 1.0 CG B:GLU727 4.8 15.8 1.0 CD2 B:HIS656 4.8 15.7 1.0 CD B:GLU727 4.9 24.4 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