Magnesium in PDB 5znl: Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6

All present enzymatic activity of Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6, PDB code: 5znl was solved by Z.Li, Y.Huang, C.G.Zhan, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.10 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.151, 81.328, 158.207, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 30.7

The structure of Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6 (pdb code 5znl). 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 PDE10A Catalytic Domain Complexed with Lhb-6, PDB code: 5znl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6


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 PDE10A Catalytic Domain Complexed with Lhb-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:20.8 occ:1.00 O A:HOH901 1.9 17.1 1.0 O A:HOH924 2.0 10.5 1.0 O A:HOH910 2.0 12.6 1.0 O A:HOH911 2.1 6.2 1.0 OD1 A:ASP564 2.3 24.4 1.0 O A:HOH907 2.7 35.1 1.0 CG A:ASP564 3.3 24.4 1.0 OE2 A:GLU592 3.5 29.9 1.0 OD2 A:ASP564 3.6 24.4 1.0 ZN A:ZN801 3.9 32.7 1.0 NE2 A:HIS595 4.3 24.7 1.0 CD2 A:HIS567 4.4 25.0 1.0 NE2 A:HIS567 4.4 24.7 1.0 CD A:GLU592 4.5 30.6 1.0 OG1 A:THR633 4.5 24.7 1.0 CD2 A:HIS563 4.5 24.7 1.0 OD2 A:ASP674 4.5 21.2 1.0 O A:HOH903 4.5 16.4 1.0 CD2 A:HIS595 4.5 25.2 1.0 CB A:ASP564 4.6 24.6 1.0 CG A:GLU592 4.7 30.2 1.0 O A:HIS563 4.7 25.4 1.0 NE2 A:HIS525 4.7 20.8 1.0 O A:THR633 4.8 24.5 1.0 CB A:THR633 4.8 24.7 1.0 CD2 A:HIS525 4.8 20.8 1.0 NE2 A:HIS563 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6


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 PDE10A Catalytic Domain Complexed with Lhb-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:14.5 occ:1.00 O B:HOH917 1.9 10.4 1.0 O B:HOH902 1.9 11.1 1.0 O B:HOH921 1.9 9.7 1.0 O B:HOH909 2.0 12.2 1.0 OD1 B:ASP564 2.2 19.1 1.0 O B:HOH906 2.3 25.3 1.0 CG B:ASP564 3.1 19.5 1.0 OE2 B:GLU592 3.4 33.1 1.0 OD2 B:ASP564 3.4 19.1 1.0 ZN B:ZN801 3.6 34.6 1.0 O B:HOH918 3.9 37.3 1.0 NE2 B:HIS595 4.3 23.9 1.0 O B:THR633 4.3 24.8 1.0 CD2 B:HIS563 4.3 18.6 1.0 CD2 B:HIS595 4.4 23.9 1.0 CD B:GLU592 4.4 33.4 1.0 OG1 B:THR633 4.5 25.7 1.0 O B:HIS563 4.5 20.7 1.0 CB B:ASP564 4.5 19.7 1.0 O B:HOH923 4.5 9.7 1.0 NE2 B:HIS525 4.7 25.0 1.0 CD2 B:HIS525 4.7 25.2 1.0 OD2 B:ASP674 4.7 20.9 1.0 NE2 B:HIS563 4.7 18.5 1.0 CB B:THR633 4.7 25.7 1.0 CD2 B:HIS567 4.8 26.2 1.0 CG B:GLU592 4.8 32.5 1.0 CA B:ASP564 4.9 19.9 1.0 OD1 B:ASP674 4.9 20.6 1.0 C B:THR633 5.0 25.1 1.0 NE2 B:HIS567 5.0 26.8 1.0

Z.Li, Y.Huang, Y.Wu, J.Chen, D.Wu, C.G.Zhan, H.B.Luo. Absolute Binding Free Energy Calculation and Design of A Subnanomolar Inhibitor of Phosphodiesterase-10. J. Med. Chem. V. 62 2099 2019.
ISSN: ISSN 1520-4804
PubMed: 30689375
DOI: 10.1021/ACS.JMEDCHEM.8B01763