Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PDE9A(Q453E) in Complex with Ibmx, PDB code: 3qi4:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg536 b:47.4 occ:1.00 OD1 A:ASP293 2.1 38.0 1.0 O A:HOH541 2.5 30.4 1.0 O A:HOH540 2.5 41.0 1.0 O A:HOH538 2.5 83.5 1.0 O A:HOH542 2.7 34.9 1.0 O A:HOH539 2.7 36.1 1.0 CG A:ASP293 2.9 33.8 1.0 OD2 A:ASP293 3.0 40.1 1.0 ZN A:ZN535 3.3 59.6 1.0 O A:HOH537 3.3 42.8 1.0 CD2 A:HIS252 4.0 30.4 1.0 NE2 A:HIS252 4.1 31.3 1.0 CD2 A:HIS292 4.1 41.8 1.0 CD2 A:HIS296 4.2 25.6 1.0 NE2 A:HIS292 4.2 48.2 1.0 NE2 A:HIS325 4.3 19.4 1.0 CB A:ASP293 4.3 33.7 1.0 O A:HIS292 4.5 31.7 1.0 NE2 A:HIS296 4.5 25.2 1.0 O A:HOH543 4.5 53.2 1.0 OD1 A:ASP402 4.5 48.4 1.0 O A:HOH549 4.6 39.6 1.0 OD2 A:ASP402 4.7 39.7 1.0 OE2 A:GLU322 4.7 26.4 1.0 OG1 A:THR363 4.7 26.2 1.0 CD2 A:HIS325 4.8 20.9 1.0 CA A:ASP293 4.8 32.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg536 b:43.5 occ:1.00 OD1 B:ASP293 2.1 41.1 1.0 O B:HOH539 2.4 36.0 1.0 O B:HOH540 2.5 46.2 1.0 O B:HOH541 2.6 29.8 1.0 O B:HOH538 2.7 57.3 1.0 O B:HOH542 2.7 67.1 1.0 CG B:ASP293 3.0 38.2 1.0 OD2 B:ASP293 3.1 45.1 1.0 ZN B:ZN535 3.5 64.1 1.0 CD2 B:HIS292 3.8 41.5 1.0 OD2 B:ASP402 4.1 43.0 1.0 NE2 B:HIS292 4.2 48.8 1.0 OG1 B:THR363 4.3 31.6 1.0 OE2 B:GLU322 4.3 34.5 1.0 CB B:ASP293 4.4 34.9 1.0 O B:HIS292 4.4 33.6 1.0 NE2 B:HIS325 4.4 25.8 1.0 CD2 B:HIS252 4.4 32.9 1.0 NE2 B:HIS252 4.6 33.3 1.0 OD1 B:ASP402 4.6 46.8 1.0 CD2 B:HIS296 4.6 29.7 1.0 CD2 B:HIS325 4.7 24.6 1.0 O B:THR363 4.7 31.0 1.0 CB B:THR363 4.8 29.9 1.0 CG B:ASP402 4.8 38.9 1.0 CA B:ASP293 4.8 33.3 1.0 CG B:HIS292 4.9 39.9 1.0 NE2 B:HIS296 5.0 29.9 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