Zinc in PDB 6b96: Crystal Structure of PDE2 in Complex with Compound 16

All present enzymatic activity of Crystal Structure of PDE2 in Complex with Compound 16:
3.1.4.17;

The structure of Crystal Structure of PDE2 in Complex with Compound 16, PDB code: 6b96 was solved by J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.29 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.330, 96.710, 102.350, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.7

The structure of Crystal Structure of PDE2 in Complex with Compound 16 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE2 in Complex with Compound 16 (pdb code 6b96). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE2 in Complex with Compound 16, PDB code: 6b96:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE2 in Complex with Compound 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE2 in Complex with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.0 occ:1.00 NE2 A:HIS696 2.0 22.2 1.0 OD2 A:ASP697 2.1 21.0 1.0 NE2 A:HIS660 2.1 18.6 1.0 OD1 A:ASP808 2.2 21.1 1.0 O A:HOH1107 2.4 21.6 1.0 O A:HOH1162 2.4 22.1 1.0 CD2 A:HIS696 2.9 21.8 1.0 CE1 A:HIS696 3.1 22.1 1.0 CD2 A:HIS660 3.1 19.3 1.0 CG A:ASP697 3.1 18.2 1.0 CE1 A:HIS660 3.1 18.3 1.0 CG A:ASP808 3.2 22.8 1.0 OD2 A:ASP808 3.5 28.4 1.0 OD1 A:ASP697 3.6 16.7 1.0 MG A:MG1002 4.0 22.0 1.0 CG A:HIS696 4.1 20.0 1.0 O A:HOH1141 4.1 23.9 1.0 CD2 A:HIS656 4.2 21.1 1.0 ND1 A:HIS696 4.2 22.1 1.0 CG A:HIS660 4.2 18.0 1.0 O A:HOH1157 4.3 18.1 1.0 ND1 A:HIS660 4.3 18.6 1.0 CB A:ASP697 4.3 15.8 1.0 NE2 A:HIS656 4.4 20.8 1.0 CB A:ASP808 4.5 19.5 1.0 CG2 A:VAL664 4.7 18.7 1.0 O A:HOH1102 4.8 19.6 1.0 CA A:ASP808 4.9 18.7 1.0 O A:ASP808 5.0 19.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE2 in Complex with Compound 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE2 in Complex with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:26.4 occ:1.00 NE2 B:HIS696 2.1 21.4 1.0 OD2 B:ASP697 2.1 21.3 1.0 NE2 B:HIS660 2.1 16.7 1.0 OD1 B:ASP808 2.2 21.4 1.0 O B:HOH1110 2.4 20.6 1.0 O B:HOH1156 2.5 23.3 1.0 CD2 B:HIS696 3.0 21.0 1.0 CE1 B:HIS660 3.1 16.6 1.0 CG B:ASP697 3.1 19.1 1.0 CE1 B:HIS696 3.1 20.9 1.0 CD2 B:HIS660 3.2 18.1 1.0 CG B:ASP808 3.2 25.3 1.0 OD2 B:ASP808 3.5 28.0 1.0 OD1 B:ASP697 3.6 18.5 1.0 MG B:MG1002 3.9 21.0 1.0 CG B:HIS696 4.1 20.0 1.0 CD2 B:HIS656 4.1 22.3 1.0 O B:HOH1153 4.2 22.3 1.0 ND1 B:HIS696 4.2 21.1 1.0 ND1 B:HIS660 4.2 18.0 1.0 CG B:HIS660 4.3 18.2 1.0 O B:HOH1218 4.3 20.0 1.0 NE2 B:HIS656 4.3 21.8 1.0 CB B:ASP697 4.3 18.2 1.0 CB B:ASP808 4.6 18.1 1.0 CG2 B:VAL664 4.7 15.7 1.0 O B:HOH1107 4.8 18.2 1.0 CA B:ASP808 4.9 17.4 1.0 O B:ASP808 4.9 19.2 1.0

A.B.Forster, P.Abeywickrema, J.Bunda, C.D.Cox, T.D.Cabalu, M.Egbertson, J.Fay, K.Getty, D.Hall, M.Kornienko, J.Lu, G.Parthasarathy, J.Reid, S.Sharma, W.D.Shipe, S.M.Smith, S.Soisson, S.J.Stachel, H.P.Su, D.Wang, R.Berger. The Identification of A Novel Lead Class For Phosphodiesterase 2 Inhibition By Fragment-Based Drug Design. Bioorg. Med. Chem. Lett. V. 27 5167 2017.
ISSN: ESSN 1464-3405
PubMed: 29113762
DOI: 10.1016/J.BMCL.2017.10.054