Magnesium in PDB 5uwf: Crystal Structure of Human PDE10A in Complex with Inhibitor 16D

All present enzymatic activity of Crystal Structure of Human PDE10A in Complex with Inhibitor 16D:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of Human PDE10A in Complex with Inhibitor 16D, PDB code: 5uwf was solved by R.Xu, E.P.Cedervall, V.Sridhar, R.Barker, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.40 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.718, 81.239, 158.609, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.8

The structure of Crystal Structure of Human PDE10A in Complex with Inhibitor 16D also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human PDE10A in Complex with Inhibitor 16D (pdb code 5uwf). 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 Human PDE10A in Complex with Inhibitor 16D, PDB code: 5uwf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human PDE10A in Complex with Inhibitor 16D


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 Human PDE10A in Complex with Inhibitor 16D within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg803 b:17.2 occ:1.00 O C:HOH984 2.0 16.7 1.0 O C:HOH993 2.2 21.9 1.0 O C:HOH915 2.2 18.6 1.0 O C:HOH989 2.2 21.2 1.0 OD1 C:ASP564 2.2 16.5 1.0 O C:HOH917 2.3 19.9 1.0 CG C:ASP564 3.2 15.9 1.0 OD2 C:ASP564 3.5 19.5 1.0 ZN C:ZN802 3.7 22.2 1.0 OE2 C:GLU592 4.0 22.4 1.0 NE2 C:HIS595 4.1 18.8 1.0 O C:HOH1025 4.2 21.0 1.0 O C:HOH1051 4.2 31.1 1.0 CD2 C:HIS563 4.2 15.5 1.0 O C:HOH947 4.2 30.0 1.0 OG1 C:THR633 4.3 19.3 1.0 O C:HIS563 4.3 18.0 1.0 CD2 C:HIS595 4.3 16.1 1.0 O C:THR633 4.4 17.1 1.0 CD2 C:HIS567 4.4 23.2 1.0 NE2 C:HIS525 4.5 18.3 1.0 OD2 C:ASP674 4.5 20.7 1.0 CB C:ASP564 4.5 16.9 1.0 CD2 C:HIS525 4.5 22.4 1.0 NE2 C:HIS563 4.6 16.2 1.0 NE2 C:HIS567 4.7 22.7 1.0 CB C:THR633 4.8 12.2 1.0 CA C:ASP564 4.8 23.3 1.0 CD C:GLU592 4.9 25.1 1.0 CG C:GLU592 4.9 19.5 1.0 O C:HOH1040 5.0 20.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human PDE10A in Complex with Inhibitor 16D


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 Human PDE10A in Complex with Inhibitor 16D within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg803 b:19.2 occ:1.00 O D:HOH946 2.0 19.4 1.0 OD1 D:ASP564 2.2 25.1 1.0 O D:HOH1008 2.2 20.9 1.0 O D:HOH907 2.3 17.7 1.0 O D:HOH901 2.3 23.8 1.0 O D:HOH909 2.4 24.3 1.0 CG D:ASP564 3.2 29.6 1.0 OD2 D:ASP564 3.5 20.4 1.0 ZN D:ZN802 3.7 25.6 1.0 OE2 D:GLU592 4.0 28.1 1.0 NE2 D:HIS595 4.0 22.2 1.0 O D:HOH1036 4.2 31.6 1.0 O D:HOH948 4.2 30.4 1.0 CD2 D:HIS525 4.2 27.2 1.0 OG1 D:THR633 4.2 22.7 1.0 NE2 D:HIS525 4.3 23.9 1.0 CD2 D:HIS595 4.3 21.9 1.0 O D:HIS563 4.3 24.0 1.0 CD2 D:HIS563 4.3 21.7 1.0 CD2 D:HIS567 4.4 24.6 1.0 OD2 D:ASP674 4.4 24.4 1.0 CB D:ASP564 4.5 22.6 1.0 O D:THR633 4.5 22.0 1.0 NE2 D:HIS567 4.6 23.6 1.0 NE2 D:HIS563 4.7 21.7 1.0 CB D:THR633 4.8 26.0 1.0 CA D:ASP564 4.8 20.4 1.0 CD D:GLU592 4.9 28.0 1.0 CG D:GLU592 4.9 27.2 1.0 O D:HOH1059 5.0 33.1 1.0

B.Dyck, B.Branstetter, T.Gharbaoui, A.R.Hudson, J.G.Breitenbucher, L.Gomez, I.Botrous, T.Marrone, R.Barido, C.K.Allerston, E.P.Cedervall, R.Xu, V.Sridhar, R.Barker, K.Aertgeerts, K.Schmelzer, D.Neul, D.Lee, M.E.Massari, C.B.Andersen, K.Sebring, X.Zhou, R.Petroski, J.Limberis, M.Augustin, L.E.Chun, T.E.Edwards, M.Peters, A.Tabatabaei. Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. J. Med. Chem. V. 60 3472 2017.
ISSN: ISSN 1520-4804
PubMed: 28406621
DOI: 10.1021/ACS.JMEDCHEM.7B00302