Sodium in PDB 6ezf: PDE2 in Complex with Molecule 5

All present enzymatic activity of PDE2 in Complex with Molecule 5:
3.1.4.17;

The structure of PDE2 in Complex with Molecule 5, PDB code: 6ezf was solved by G.Tresadern, L.Perez-Benito, H.Keraenen, H.Van Vlijmen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.37 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.239, 65.315, 104.391, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.8

The structure of PDE2 in Complex with Molecule 5 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the PDE2 in Complex with Molecule 5 (pdb code 6ezf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the PDE2 in Complex with Molecule 5, PDB code: 6ezf:

Sodium binding site 1 out of 1 in the PDE2 in Complex with Molecule 5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PDE2 in Complex with Molecule 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1007 b:34.0 occ:1.00 O A:HOH1302 1.9 17.8 1.0 O A:HOH1376 2.1 17.8 1.0 NE2 A:HIS656 2.3 16.5 1.0 CE1 A:HIS656 3.2 16.4 1.0 CD2 A:HIS656 3.3 17.1 1.0 O A:HOH1181 3.4 16.2 1.0 O A:HOH1278 3.7 22.1 1.0 MG A:MG1001 3.8 15.4 1.0 ZN A:ZN1002 3.8 14.2 0.8 O A:HOH1286 3.8 23.9 1.0 O A:HOH1425 3.9 46.3 1.0 OD2 A:ASP697 4.3 14.3 1.0 O A:HOH1216 4.3 18.0 1.0 O A:HOH1432 4.3 30.6 1.0 ND1 A:HIS656 4.4 16.1 1.0 CG A:HIS656 4.4 15.4 1.0 OD2 A:ASP808 4.5 22.5 1.0 O A:HOH1335 4.6 21.6 1.0 CE2 A:TYR655 4.6 17.0 1.0 OD1 A:ASP808 4.6 14.9 1.0 OD1 A:ASP697 4.8 14.4 1.0 NE2 A:HIS660 4.8 12.6 1.0 CG A:ASP697 4.9 13.7 1.0 O A:HOH1275 4.9 17.6 1.0 CD2 A:TYR655 5.0 16.6 1.0 CG A:ASP808 5.0 15.4 1.0

L.Perez-Benito, H.Keranen, H.Van Vlijmen, G.Tresadern. Predicting Binding Free Energies of PDE2 Inhibitors. the Difficulties of Protein Conformation. Sci Rep V. 8 4883 2018.
ISSN: ESSN 2045-2322
PubMed: 29559702
DOI: 10.1038/S41598-018-23039-5