Magnesium in PDB 5k9r: PDE10A with Imidazopyrazine Inhibitor

All present enzymatic activity of PDE10A with Imidazopyrazine Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of PDE10A with Imidazopyrazine Inhibitor, PDB code: 5k9r was solved by A.G.Gibbs, C.Schubert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.460, 81.200, 160.150, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 32.2

The structure of PDE10A with Imidazopyrazine Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the PDE10A with Imidazopyrazine Inhibitor (pdb code 5k9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PDE10A with Imidazopyrazine Inhibitor, PDB code: 5k9r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the PDE10A with Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE10A with Imidazopyrazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:24.3 occ:1.00 O A:HOH913 1.8 22.0 1.0 O A:HOH912 2.0 35.6 1.0 OD1 A:ASP554 2.1 35.2 1.0 O A:HOH904 2.5 26.8 1.0 OE1 A:GLU582 3.1 41.9 1.0 CG A:ASP554 3.3 37.2 1.0 NE2 A:HIS585 3.4 42.5 1.0 CD2 A:HIS585 3.8 41.9 1.0 OD2 A:ASP554 3.9 38.3 1.0 CD A:GLU582 4.0 41.2 1.0 O A:HIS553 4.1 36.1 1.0 CG A:GLU582 4.2 41.0 1.0 CD2 A:HIS557 4.2 37.9 1.0 NE2 A:HIS557 4.3 37.7 1.0 OG1 A:THR623 4.3 34.6 1.0 ZN A:ZN801 4.5 40.5 1.0 CB A:ASP554 4.5 36.8 1.0 CE1 A:HIS585 4.6 42.8 1.0 CD2 A:HIS515 4.6 37.6 1.0 O A:THR623 4.6 36.3 1.0 CD2 A:HIS553 4.7 34.2 1.0 NE2 A:HIS515 4.8 37.4 1.0 CA A:ASP554 4.8 36.7 1.0

Magnesium binding site 2 out of 2 in the PDE10A with Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE10A with Imidazopyrazine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:28.1 occ:1.00 OD1 B:ASP554 1.9 35.8 1.0 O B:HOH905 2.0 22.7 1.0 O B:HOH902 2.0 20.5 1.0 O B:HOH903 2.1 5.5 1.0 O B:HOH912 2.4 18.6 1.0 CG B:ASP554 2.9 38.8 1.0 OD2 B:ASP554 3.3 38.9 1.0 OE1 B:GLU582 3.5 45.4 1.0 ZN B:ZN801 3.8 43.5 1.0 OG1 B:THR623 3.9 42.7 1.0 CD2 B:HIS553 4.0 40.1 1.0 O B:HIS553 4.0 39.9 1.0 CE1 B:HIS585 4.0 50.1 1.0 OD2 B:ASP664 4.1 33.5 1.0 O B:HOH907 4.2 35.5 1.0 NE2 B:HIS515 4.2 41.4 1.0 CB B:ASP554 4.3 40.2 1.0 CB B:THR623 4.3 42.2 1.0 CD2 B:HIS515 4.4 41.2 1.0 ND1 B:HIS585 4.4 50.6 1.0 CD B:GLU582 4.5 45.9 1.0 NE2 B:HIS553 4.6 40.6 1.0 O B:HOH913 4.6 14.5 1.0 CA B:ASP554 4.6 40.4 1.0 CD2 B:HIS557 4.6 45.2 1.0 O B:THR623 4.7 43.1 1.0 C B:HIS553 4.8 39.8 1.0 CG B:GLU582 4.8 46.8 1.0 NE2 B:HIS557 4.9 45.1 1.0 NE2 B:HIS585 4.9 50.1 1.0

S.K.Meegalla, H.Huang, C.R.Illig, D.J.Parks, J.Chen, Y.K.Lee, K.J.Wilson, S.K.Patel, W.S.Cheung, T.Lu, T.Kirchner, H.B.Askari, J.Geisler, R.J.Patch, A.C.Gibbs, B.Rady, M.Connelly, M.R.Player. Discovery of Novel Potent Imidazo[1,2-B]Pyridazine PDE10A Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4216 2016.
ISSN: ESSN 1464-3405
PubMed: 27491708
DOI: 10.1016/J.BMCL.2016.07.054