Zinc in PDB 3qi4: Crystal Structure of PDE9A(Q453E) in Complex with Ibmx

All present enzymatic activity of Crystal Structure of PDE9A(Q453E) in Complex with Ibmx:
3.1.4.35;

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Ibmx, PDB code: 3qi4 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 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.409, 103.409, 269.950, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.9

The structure of Crystal Structure of PDE9A(Q453E) in Complex with Ibmx also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE9A(Q453E) in Complex with Ibmx (pdb code 3qi4). 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 Ibmx, PDB code: 3qi4:
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 Ibmx


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 Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn535 b:59.6 occ:1.00 OD2 A:ASP293 2.1 40.1 1.0 OD1 A:ASP402 2.1 48.4 1.0 NE2 A:HIS292 2.1 48.2 1.0 NE2 A:HIS256 2.1 41.5 1.0 O A:HOH537 2.6 42.8 1.0 CE1 A:HIS292 3.1 44.2 1.0 CD2 A:HIS256 3.1 34.6 1.0 CD2 A:HIS292 3.1 41.8 1.0 CE1 A:HIS256 3.1 35.4 1.0 CG A:ASP293 3.2 33.8 1.0 CG A:ASP402 3.2 38.5 1.0 MG A:MG536 3.3 47.4 1.0 O A:HOH538 3.4 83.5 1.0 OD2 A:ASP402 3.7 39.7 1.0 OD1 A:ASP293 3.7 38.0 1.0 ND1 A:HIS292 4.2 42.0 1.0 CD2 A:HIS252 4.2 30.4 1.0 CG A:HIS292 4.2 40.1 1.0 O A:HOH551 4.2 41.6 1.0 ND1 A:HIS256 4.2 34.0 1.0 CG A:HIS256 4.2 35.0 1.0 CB A:ASP293 4.4 33.7 1.0 O A:ASP402 4.5 35.8 1.0 CB A:ASP402 4.5 36.2 1.0 NE2 A:HIS252 4.5 31.3 1.0 O A:HOH541 4.5 30.4 1.0 CG2 A:VAL260 4.7 20.8 1.0 O A:HOH549 4.8 39.6 1.0 CA A:ASP402 4.9 34.4 1.0 O A:HOH540 4.9 41.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of PDE9A(Q453E) in Complex with Ibmx


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 Ibmx within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn535 b:64.1 occ:1.00 OD2 B:ASP293 2.1 45.1 1.0 OD1 B:ASP402 2.1 46.8 1.0 NE2 B:HIS292 2.1 48.8 1.0 NE2 B:HIS256 2.1 47.1 1.0 O B:HOH542 2.9 67.1 1.0 CD2 B:HIS292 3.0 41.5 1.0 CD2 B:HIS256 3.0 39.9 1.0 CG B:ASP402 3.1 38.9 1.0 CE1 B:HIS292 3.1 43.9 1.0 CE1 B:HIS256 3.2 40.3 1.0 CG B:ASP293 3.2 38.2 1.0 OD2 B:ASP402 3.5 43.0 1.0 MG B:MG536 3.5 43.5 1.0 O B:HOH537 3.8 38.1 1.0 OD1 B:ASP293 3.8 41.1 1.0 CG B:HIS292 4.2 39.9 1.0 ND1 B:HIS292 4.2 41.5 1.0 CG B:HIS256 4.2 39.2 1.0 CD2 B:HIS252 4.2 32.9 1.0 ND1 B:HIS256 4.3 38.8 1.0 O B:ASP402 4.3 32.9 1.0 CB B:ASP293 4.4 34.9 1.0 CB B:ASP402 4.4 36.6 1.0 NE2 B:HIS252 4.6 33.3 1.0 CG2 B:VAL260 4.6 22.8 1.0 CA B:ASP402 4.7 33.9 1.0 C B:ASP402 4.9 32.5 1.0 O B:HOH539 4.9 36.0 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 E1809 2011.
ISSN: ESSN 1932-6203
PubMed: 21483814
DOI: 10.1371/JOURNAL.PONE.0018092