Magnesium 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
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the PDE9A Catalytic Domain in Complex with (R)- BAY73-6691, PDB code: 3k3e:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:37.1 occ:1.00 OD1 A:ASP293 2.1 38.0 1.0 O A:HOH706 2.3 35.8 1.0 O A:HOH702 2.4 35.9 1.0 O A:HOH705 2.5 38.3 1.0 O A:HOH703 2.5 34.4 1.0 O A:HOH704 2.6 48.4 1.0 CG A:ASP293 3.2 36.7 1.0 OD2 A:ASP293 3.6 36.1 1.0 O A:HOH707 3.7 28.3 1.0 NE2 A:HIS325 3.8 43.8 1.0 OE2 A:GLU322 3.8 42.1 1.0 ZN A:ZN601 4.0 44.4 1.0 CD2 A:HIS296 4.0 46.3 1.0 CD2 A:HIS325 4.0 43.3 1.0 O A:HIS292 4.2 41.3 1.0 CD2 A:HIS292 4.3 40.2 1.0 CD2 A:HIS252 4.4 48.0 1.0 NE2 A:HIS296 4.4 45.0 1.0 CB A:ASP293 4.5 37.1 1.0 NE2 A:HIS252 4.5 49.8 1.0 O A:HOH701 4.5 38.5 1.0 OG1 A:THR363 4.6 36.8 1.0 CA A:ASP293 4.7 37.8 1.0 NE2 A:HIS292 4.8 41.3 1.0 CD A:GLU322 4.8 44.3 1.0 OD2 A:ASP402 4.8 32.2 1.0 CE1 A:HIS325 4.9 44.8 1.0 C A:HIS292 5.0 41.6 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:50.0 occ:1.00 OD1 B:ASP293 2.1 50.4 1.0 O B:HOH715 2.4 30.6 1.0 O B:HOH713 2.6 46.2 1.0 O B:HOH714 2.7 35.0 1.0 O B:HOH712 2.8 46.3 1.0 CG B:ASP293 3.0 48.7 1.0 O B:HOH711 3.2 52.5 1.0 OD2 B:ASP293 3.2 48.7 1.0 ZN B:ZN601 3.3 47.5 1.0 CD2 B:HIS292 4.0 42.1 1.0 OD2 B:ASP402 4.1 37.6 1.0 CD2 B:HIS252 4.3 46.6 1.0 OE2 B:GLU322 4.4 46.2 1.0 NE2 B:HIS292 4.4 41.6 1.0 NE2 B:HIS252 4.4 46.7 1.0 CD2 B:HIS296 4.4 43.1 1.0 NE2 B:HIS325 4.4 38.7 1.0 CB B:ASP293 4.5 47.8 1.0 O B:HIS292 4.5 50.5 1.0 OG1 B:THR363 4.6 35.3 1.0 CD2 B:HIS325 4.7 38.7 1.0 OD1 B:ASP402 4.7 41.1 1.0 NE2 B:HIS296 4.8 41.2 1.0 CG B:ASP402 4.8 39.2 1.0 CB B:THR363 4.9 33.8 1.0 CA B:ASP293 4.9 46.7 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