Zinc in PDB 3k3e: Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691

All present enzymatic activity of Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691:
3.1.4.35;

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691, PDB code: 3k3e was solved by H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, 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 (°)	103.190, 103.190, 270.849, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 25.8

The structure of Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691 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 the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691 (pdb code 3k3e). 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 (R)- BAY73-6691, PDB code: 3k3e:
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 (R)- BAY73-6691


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 (R)- BAY73-6691 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:44.4 occ:1.00 OD2 A:ASP293 2.0 36.1 1.0 OD1 A:ASP402 2.1 40.3 1.0 NE2 A:HIS256 2.1 40.2 1.0 NE2 A:HIS292 2.1 41.3 1.0 O A:HOH702 2.4 35.9 1.0 O A:HOH701 2.8 38.5 1.0 CD2 A:HIS292 2.9 40.2 1.0 CE1 A:HIS256 3.0 37.0 1.0 CG A:ASP402 3.0 37.8 1.0 CG A:ASP293 3.1 36.7 1.0 CD2 A:HIS256 3.2 38.2 1.0 CE1 A:HIS292 3.2 41.9 1.0 OD2 A:ASP402 3.3 32.2 1.0 OD1 A:ASP293 3.6 38.0 1.0 MG A:MG602 4.0 37.1 1.0 CG A:HIS292 4.1 41.4 1.0 O A:HOH704 4.1 48.4 1.0 ND1 A:HIS256 4.1 37.4 1.0 CD2 A:HIS252 4.2 48.0 1.0 ND1 A:HIS292 4.2 41.8 1.0 CG A:HIS256 4.3 38.1 1.0 CB A:ASP293 4.4 37.1 1.0 CB A:ASP402 4.4 38.7 1.0 NE2 A:HIS252 4.5 49.8 1.0 O A:ASP402 4.5 46.5 1.0 CG2 A:VAL260 4.7 33.8 1.0 O A:HOH705 4.8 38.3 1.0 CA A:ASP402 4.9 41.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691


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 (R)- BAY73-6691 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:47.5 occ:1.00 OD2 B:ASP293 2.0 48.7 1.0 OD1 B:ASP402 2.1 41.1 1.0 NE2 B:HIS256 2.1 43.5 1.0 NE2 B:HIS292 2.1 41.6 1.0 O B:HOH711 2.8 52.5 1.0 CD2 B:HIS292 2.8 42.1 1.0 CG B:ASP402 2.9 39.2 1.0 CE1 B:HIS256 3.0 43.2 1.0 CG B:ASP293 3.1 48.7 1.0 CD2 B:HIS256 3.1 45.0 1.0 OD2 B:ASP402 3.2 37.6 1.0 CE1 B:HIS292 3.3 41.4 1.0 MG B:MG602 3.3 50.0 1.0 OD1 B:ASP293 3.5 50.4 1.0 CG B:HIS292 4.1 44.3 1.0 ND1 B:HIS256 4.1 42.5 1.0 CG B:HIS256 4.2 45.0 1.0 ND1 B:HIS292 4.3 42.6 1.0 CB B:ASP402 4.4 39.2 1.0 CB B:ASP293 4.4 47.8 1.0 CD2 B:HIS252 4.4 46.6 1.0 O B:ASP402 4.5 44.6 1.0 O B:HOH713 4.7 46.2 1.0 CG2 B:VAL260 4.7 36.3 1.0 NE2 B:HIS252 4.8 46.7 1.0 CA B:ASP402 4.9 41.8 1.0

H.Wang, X.Luo, M.Ye, J.Hou, H.Robinson, H.Ke. Insight Into Binding of Phosphodiesterase-9A Selective Inhibitors By Crystal Structures and Mutagenesis J.Med.Chem. V. 53 1726 2010.
ISSN: ISSN 0022-2623
PubMed: 20121115
DOI: 10.1021/JM901519F