Zinc in PDB 3qi3: Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691

All present enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691:
3.1.4.35;

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3 was solved by J.Hou, J.Xu, M.Liu, R.Zhao, H.Lou, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.127, 103.127, 270.441, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.2

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor 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 PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 (pdb code 3qi3). 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 PDE9A(Q453E) in Complex with Inhibitor BAY73-6691, PDB code: 3qi3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor 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 PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn534 b:54.9 occ:1.00 OD2 A:ASP293 2.1 37.6 1.0 OD1 A:ASP402 2.1 47.7 1.0 NE2 A:HIS292 2.1 43.0 1.0 NE2 A:HIS256 2.1 46.4 1.0 O A:HOH537 2.4 39.0 1.0 O A:HOH536 2.6 39.7 1.0 CD2 A:HIS292 3.0 38.4 1.0 CD2 A:HIS256 3.1 40.7 1.0 CE1 A:HIS292 3.1 39.1 1.0 CE1 A:HIS256 3.1 42.0 1.0 CG A:ASP402 3.2 42.8 1.0 CG A:ASP293 3.2 34.9 1.0 OD2 A:ASP402 3.6 43.9 1.0 OD1 A:ASP293 3.7 34.6 1.0 MG A:MG535 3.9 42.5 1.0 CG A:HIS292 4.2 38.5 1.0 ND1 A:HIS292 4.2 39.7 1.0 ND1 A:HIS256 4.2 41.9 1.0 CG A:HIS256 4.2 40.9 1.0 CD2 A:HIS252 4.3 39.1 1.0 CB A:ASP293 4.4 34.5 1.0 CB A:ASP402 4.5 40.4 1.0 O A:HOH539 4.5 42.8 1.0 O A:ASP402 4.5 41.1 1.0 NE2 A:HIS252 4.6 38.6 1.0 O A:HOH540 4.7 46.2 1.0 CG2 A:VAL260 4.7 32.0 1.0 CA A:ASP402 4.8 40.5 1.0 O A:HOH548 4.9 52.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE9A(Q453E) in Complex with Inhibitor 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 PDE9A(Q453E) in Complex with Inhibitor BAY73-6691 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn534 b:67.1 occ:1.00 OD2 B:ASP293 2.1 51.5 1.0 OD1 B:ASP402 2.1 52.2 1.0 NE2 B:HIS292 2.1 52.5 1.0 NE2 B:HIS256 2.1 57.7 1.0 O B:HOH541 2.5 51.3 1.0 O B:HOH536 3.0 49.4 1.0 CD2 B:HIS292 3.0 46.2 1.0 CD2 B:HIS256 3.1 50.9 1.0 CG B:ASP402 3.1 46.5 1.0 CG B:ASP293 3.2 44.0 1.0 CE1 B:HIS292 3.2 48.1 1.0 CE1 B:HIS256 3.2 51.7 1.0 OD2 B:ASP402 3.5 48.3 1.0 OD1 B:ASP293 3.7 46.4 1.0 MG B:MG535 3.9 49.9 1.0 CD2 B:HIS252 4.1 40.3 1.0 CG B:HIS292 4.2 44.7 1.0 ND1 B:HIS292 4.2 47.1 1.0 CG B:HIS256 4.2 49.6 1.0 ND1 B:HIS256 4.2 50.2 1.0 CB B:ASP293 4.3 40.1 1.0 NE2 B:HIS252 4.5 41.7 1.0 CB B:ASP402 4.5 44.9 1.0 O B:HOH537 4.5 50.0 1.0 O B:ASP402 4.5 44.9 1.0 CG2 B:VAL260 4.7 27.2 1.0 CA B:ASP402 4.8 43.1 1.0 O B:HOH544 4.9 63.6 1.0 O B:HOH538 5.0 38.1 1.0

J.Hou, J.Xu, M.Liu, R.Zhao, H.B.Luo, H.Ke. Structural Asymmetry of Phosphodiesterase-9, Potential Protonation of A Glutamic Acid, and Role of the Invariant Glutamine. Plos One V. 6 18092 2011.
ISSN: ESSN 1932-6203
PubMed: 21483814
DOI: 10.1371/JOURNAL.PONE.0018092