Zinc in PDB 4y86: Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33

All present enzymatic activity of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33:
3.1.4.35;

The structure of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33, PDB code: 4y86 was solved by M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.14 / 2.01
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.135, 104.135, 269.536, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 24.7

The structure of Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33 (pdb code 4y86). 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 PDE9 in Complex with Racemic Inhibitor C33, PDB code: 4y86:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33


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 PDE9 in Complex with Racemic Inhibitor C33 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:46.8 occ:1.00 OD2 A:ASP293 2.0 33.7 1.0 OD1 A:ASP402 2.1 35.2 1.0 NE2 A:HIS292 2.2 36.8 1.0 NE2 A:HIS256 2.2 34.8 1.0 O A:HOH718 2.3 32.2 1.0 O A:HOH717 2.4 34.1 1.0 CG A:ASP402 3.0 30.9 1.0 CD2 A:HIS292 3.1 33.4 1.0 CG A:ASP293 3.1 29.6 1.0 CE1 A:HIS256 3.1 31.6 1.0 CD2 A:HIS256 3.2 31.7 1.0 CE1 A:HIS292 3.2 33.9 1.0 OD2 A:ASP402 3.3 31.9 1.0 OD1 A:ASP293 3.6 28.8 1.0 MG A:MG603 3.9 30.7 1.0 O A:HOH720 4.1 34.1 1.0 O A:HOH747 4.1 34.8 1.0 CD2 A:HIS252 4.1 28.9 1.0 CG A:HIS292 4.2 32.0 1.0 ND1 A:HIS256 4.2 31.6 1.0 ND1 A:HIS292 4.3 32.0 1.0 CB A:ASP293 4.3 27.7 1.0 CG A:HIS256 4.3 30.6 1.0 NE2 A:HIS252 4.4 29.1 1.0 CB A:ASP402 4.4 30.9 1.0 O A:ASP402 4.7 29.0 1.0 O A:HOH721 4.7 21.8 1.0 CG2 A:VAL260 4.8 28.6 1.0 CA A:ASP402 4.9 29.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE9 in Complex with Racemic Inhibitor C33


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 PDE9 in Complex with Racemic Inhibitor C33 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:49.3 occ:1.00 OD2 B:ASP293 2.0 35.4 1.0 OD1 B:ASP402 2.1 36.3 1.0 NE2 B:HIS292 2.2 37.3 1.0 NE2 B:HIS256 2.2 40.2 1.0 O B:HOH724 2.4 28.6 1.0 O B:HOH725 2.4 34.4 1.0 CG B:ASP402 3.0 32.2 1.0 CD2 B:HIS292 3.1 33.5 1.0 CE1 B:HIS256 3.1 38.1 1.0 CG B:ASP293 3.1 30.5 1.0 CE1 B:HIS292 3.2 34.9 1.0 CD2 B:HIS256 3.2 37.8 1.0 OD2 B:ASP402 3.2 34.7 1.0 OD1 B:ASP293 3.6 29.4 1.0 O B:HOH727 3.9 30.9 1.0 MG B:MG603 4.0 32.8 1.0 CD2 B:HIS252 4.1 29.0 1.0 O B:HOH756 4.1 35.5 1.0 CG B:HIS292 4.2 32.6 1.0 ND1 B:HIS256 4.2 37.2 1.0 ND1 B:HIS292 4.3 34.0 1.0 CG B:HIS256 4.3 36.9 1.0 NE2 B:HIS252 4.3 30.0 1.0 CB B:ASP293 4.3 29.4 1.0 CB B:ASP402 4.4 31.9 1.0 O B:ASP402 4.5 30.1 1.0 CG2 B:VAL260 4.7 29.1 1.0 CA B:ASP402 4.8 31.1 1.0 O B:HOH726 4.8 20.0 1.0

M.Huang, Y.Shao, J.Hou, W.Cui, B.Liang, Y.Huang, Z.Li, Y.Wu, X.Zhu, P.Liu, Y.Wan, H.Ke, H.B.Luo. Structural Asymmetry of Phosphodiesterase-9A and A Unique Pocket For Selective Binding of A Potent Enantiomeric Inhibitor. Mol.Pharmacol. V. 88 836 2015.
ISSN: ESSN 1521-0111
PubMed: 26316540
DOI: 10.1124/MOL.115.099747