Chlorine 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
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the PDE2 in Complex with Molecule 5 (pdb code 6ezf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the PDE2 in Complex with Molecule 5, PDB code: 6ezf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the PDE2 in Complex with Molecule 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of PDE2 in Complex with Molecule 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:27.1 occ:1.00 CL1 A:C6Z1003 0.0 27.1 1.0 C2 A:C6Z1003 1.7 23.8 1.0 C8 A:C6Z1003 2.7 22.2 1.0 C3 A:C6Z1003 2.7 23.2 1.0 O A:ALA717 3.2 17.1 1.0 C A:ALA717 3.4 14.2 1.0 CD2 A:LEU770 3.4 22.5 0.0 CB A:ALA717 3.5 16.9 1.0 N A:LEU718 3.8 13.5 1.0 CE1 A:PHE707 3.9 26.0 1.0 CA A:LEU718 4.0 13.9 1.0 CD2 A:LEU718 4.0 16.8 1.0 C6 A:C6Z1003 4.0 23.3 1.0 C4 A:C6Z1003 4.0 23.5 1.0 CA A:ALA717 4.0 15.4 1.0 CG A:LEU718 4.4 16.1 1.0 CE A:MET847 4.4 30.8 0.5 CD1 A:LEU770 4.5 25.7 0.5 C5 A:C6Z1003 4.5 21.5 1.0 CD1 A:PHE707 4.6 25.7 1.0 O A:HOH1213 4.7 19.9 1.0 CZ A:PHE707 4.7 26.3 1.0 CB A:LEU718 4.8 13.8 1.0 CG A:LEU770 4.8 21.9 0.5 CE A:MET847 4.8 16.4 0.5 CE1 A:PHE862 4.9 16.6 1.0 O A:HOH1377 5.0 43.3 1.0 CD1 A:PHE862 5.0 15.7 1.0

Chlorine binding site 2 out of 2 in the PDE2 in Complex with Molecule 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of PDE2 in Complex with Molecule 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:26.6 occ:1.00 CL7 A:C6Z1003 0.0 26.6 1.0 C6 A:C6Z1003 1.7 23.3 1.0 C8 A:C6Z1003 2.7 22.2 1.0 C5 A:C6Z1003 2.8 21.5 1.0 C9 A:C6Z1003 3.2 22.7 1.0 O A:HOH1105 3.4 41.2 1.0 OH A:TYR827 3.5 25.1 1.0 C10 A:C6Z1003 3.8 23.6 1.0 N11 A:C6Z1003 3.8 26.5 1.0 C2 A:C6Z1003 4.0 23.8 1.0 CG2 A:VAL714 4.0 19.1 1.0 C4 A:C6Z1003 4.0 23.5 1.0 CB A:PHE862 4.1 14.2 1.0 CD1 A:PHE862 4.2 15.7 1.0 CE A:MET847 4.2 30.8 0.5 O A:LEU858 4.2 14.4 1.0 SD A:MET847 4.3 19.9 0.5 C3 A:C6Z1003 4.5 23.2 1.0 CG A:PHE862 4.5 15.4 1.0 CB A:LEU858 4.6 13.0 1.0 CB A:MET847 4.6 19.5 0.5 CB A:MET847 4.7 18.9 0.5 CD2 A:LEU858 4.7 18.6 1.0 CZ A:TYR827 4.7 18.7 1.0 C A:LEU858 4.8 14.9 1.0 N12 A:C6Z1003 4.8 25.8 1.0 CG A:MET847 4.8 23.1 0.5 C16 A:C6Z1003 4.9 24.7 1.0 CG A:MET847 4.9 20.3 0.5 CD2 A:LEU718 5.0 16.8 1.0 CE2 A:PHE830 5.0 18.6 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