Zinc in PDB 4gh6: Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28

All present enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28:
3.1.4.35;

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28, PDB code: 4gh6 was solved by J.Hou, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.276, 104.276, 270.073, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.5

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28 (pdb code 4gh6). 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 the PDE9A Catalytic Domain in Complex with Inhibitor 28, PDB code: 4gh6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28


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 the PDE9A Catalytic Domain in Complex with Inhibitor 28 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:60.4 occ:1.00 OD2 A:ASP293 2.1 42.8 1.0 OD1 A:ASP402 2.1 47.3 1.0 NE2 A:HIS292 2.1 40.5 1.0 NE2 A:HIS256 2.1 42.6 1.0 O A:HOH701 2.4 37.8 1.0 O A:HOH702 2.4 34.2 1.0 CD2 A:HIS292 2.9 34.6 1.0 CG A:ASP402 3.0 42.6 1.0 CE1 A:HIS256 3.1 35.1 1.0 CD2 A:HIS256 3.1 36.4 1.0 CG A:ASP293 3.2 36.3 1.0 CE1 A:HIS292 3.2 34.0 1.0 OD2 A:ASP402 3.3 43.6 1.0 OD1 A:ASP293 3.7 42.0 1.0 MG A:MG603 4.0 43.2 1.0 CG A:HIS292 4.1 34.6 1.0 ND1 A:HIS256 4.2 35.1 1.0 ND1 A:HIS292 4.3 33.1 1.0 CG A:HIS256 4.3 35.1 1.0 CD2 A:HIS252 4.3 37.8 1.0 CB A:ASP293 4.4 36.3 1.0 CB A:ASP402 4.4 43.9 1.0 O A:HOH704 4.4 33.1 1.0 O A:HOH705 4.5 30.7 1.0 NE2 A:HIS252 4.5 36.9 1.0 O A:ASP402 4.6 46.4 1.0 O A:HOH709 4.6 40.7 1.0 CG2 A:VAL260 4.7 31.9 1.0 CA A:ASP402 4.8 44.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with Inhibitor 28


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 the PDE9A Catalytic Domain in Complex with Inhibitor 28 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:61.7 occ:1.00 OD2 B:ASP293 2.1 48.5 1.0 OD1 B:ASP402 2.1 47.9 1.0 NE2 B:HIS292 2.1 46.8 1.0 NE2 B:HIS256 2.1 47.3 1.0 O B:HOH702 2.5 48.3 1.0 O B:HOH701 2.6 27.0 1.0 CD2 B:HIS292 3.0 41.4 1.0 CG B:ASP402 3.0 42.7 1.0 CE1 B:HIS256 3.0 41.7 1.0 CD2 B:HIS256 3.1 41.6 1.0 CE1 B:HIS292 3.2 41.1 1.0 CG B:ASP293 3.2 42.2 1.0 OD2 B:ASP402 3.2 44.5 1.0 OD1 B:ASP293 3.8 43.3 1.0 CD2 B:HIS252 4.1 35.9 1.0 ND1 B:HIS256 4.2 41.2 1.0 CG B:HIS292 4.2 42.0 1.0 CG B:HIS256 4.2 41.5 1.0 ND1 B:HIS292 4.3 39.9 1.0 O B:HOH704 4.3 51.3 1.0 MG B:MG604 4.3 36.6 1.0 O B:ASP402 4.3 42.5 1.0 NE2 B:HIS252 4.3 34.6 1.0 CB B:ASP402 4.4 40.5 1.0 CB B:ASP293 4.4 41.8 1.0 CG2 B:VAL260 4.7 37.9 1.0 CA B:ASP402 4.9 39.6 1.0 O B:HOH703 4.9 35.9 1.0

F.Meng, J.Hou, Y.X.Shao, P.Y.Wu, M.Huang, X.Zhu, Y.Cai, Z.Li, J.Xu, P.Liu, H.B.Luo, Y.Wan, H.Ke. Structure-Based Discovery of Highly Selective Phosphodiesterase-9A Inhibitors and Implications For Inhibitor Design. J.Med.Chem. V. 55 8549 2012.
ISSN: ISSN 0022-2623
PubMed: 22985069
DOI: 10.1021/JM301189C