Zinc in PDB 6lzz: Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A

All present enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A:
3.1.4.35;

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A, PDB code: 6lzz was solved by Y.Y.Huang, Y.Wu, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.87 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.383, 103.383, 268.366, 90, 90, 90
R / Rfree (%)	25.3 / 29.5

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A (pdb code 6lzz). 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 PDE9 Catalytic Domain in Complex with Inhibitor 4A, PDB code: 6lzz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A


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 PDE9 Catalytic Domain in Complex with Inhibitor 4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:54.5 occ:1.00 OD1 A:ASP402 2.2 28.4 1.0 OD2 A:ASP293 2.2 24.9 1.0 NE2 A:HIS256 2.3 32.1 1.0 O A:HOH732 2.4 23.0 1.0 NE2 A:HIS292 2.7 22.4 1.0 CE1 A:HIS256 3.1 23.5 1.0 CG A:ASP402 3.2 24.7 1.0 CG A:ASP293 3.3 23.6 1.0 CD2 A:HIS292 3.3 21.6 1.0 CD2 A:HIS256 3.4 27.1 1.0 OD2 A:ASP402 3.4 23.9 1.0 OD1 A:ASP293 3.6 21.7 1.0 CE1 A:HIS292 3.9 23.5 1.0 O A:HOH730 3.9 34.1 1.0 CD2 A:HIS252 4.0 21.8 1.0 MG A:MG602 4.0 23.9 1.0 NE2 A:HIS252 4.1 26.8 1.0 O A:HOH763 4.1 20.9 1.0 ND1 A:HIS256 4.3 27.3 1.0 CG A:HIS256 4.4 28.1 1.0 O A:HOH706 4.5 24.8 1.0 CB A:ASP402 4.5 26.6 1.0 CB A:ASP293 4.5 22.3 1.0 CG A:HIS292 4.6 25.2 1.0 O A:ASP402 4.6 22.8 1.0 ND1 A:HIS292 4.8 22.4 1.0 CA A:ASP402 4.8 25.4 1.0 CG2 A:VAL260 4.9 22.3 1.0 O A:HOH716 4.9 23.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 4A


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 PDE9 Catalytic Domain in Complex with Inhibitor 4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:59.1 occ:1.00 OD2 B:ASP293 2.3 24.1 1.0 OD1 B:ASP402 2.4 27.4 1.0 O B:HOH769 2.5 33.0 1.0 NE2 B:HIS256 2.5 26.1 1.0 NE2 B:HIS292 2.6 29.3 1.0 CD2 B:HIS292 3.2 26.4 1.0 MG B:MG602 3.3 20.2 1.0 CG B:ASP293 3.4 22.6 1.0 CG B:ASP402 3.4 25.3 1.0 CE1 B:HIS256 3.4 23.5 1.0 CD2 B:HIS256 3.5 24.2 1.0 OD2 B:ASP402 3.6 26.9 1.0 CD2 B:HIS252 3.7 24.2 1.0 NE2 B:HIS252 3.8 26.3 1.0 CE1 B:HIS292 3.8 27.3 1.0 O B:HOH768 3.8 20.0 1.0 OD1 B:ASP293 3.9 24.8 1.0 O B:HOH727 4.1 23.7 1.0 CG B:HIS292 4.5 25.0 1.0 CB B:ASP293 4.5 25.0 1.0 ND1 B:HIS256 4.6 28.5 1.0 CG B:HIS256 4.6 23.9 1.0 O B:ASP402 4.7 25.5 1.0 O B:HOH710 4.7 19.5 1.0 CB B:ASP402 4.7 25.2 1.0 ND1 B:HIS292 4.8 25.8 1.0

Y.J.Tian, Q.Zhou, P.Zhang, M.Y.Jiang, B.Zhang, X.N.Wu, C.Zhang, Z.Li, Y.Wu, Z.Chen, H.B.Luo. Identification of Phosphodiesterase-9 As A Novel Target For Pulmonary Arterial Hypertension By Using Highly Selective and Orally Bioavailable Inhibitors To Be Published.