Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A Catalytic Domain Complexed with Lhb-6, PDB code: 5znl:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:32.7 occ:1.00 NE2 A:HIS563 2.0 24.9 1.0 OD2 A:ASP564 2.0 24.4 1.0 OD1 A:ASP674 2.2 20.8 1.0 O A:HOH910 2.4 12.6 1.0 NE2 A:HIS529 2.4 15.9 1.0 CD2 A:HIS563 2.9 24.7 1.0 CG A:ASP674 3.0 21.7 1.0 CG A:ASP564 3.1 24.4 1.0 CE1 A:HIS563 3.1 25.0 1.0 O A:HOH903 3.1 16.4 1.0 CD2 A:HIS529 3.2 15.8 1.0 OD2 A:ASP674 3.2 21.2 1.0 OD1 A:ASP564 3.5 24.4 1.0 CE1 A:HIS529 3.5 15.8 1.0 O A:HOH924 3.6 10.5 1.0 MG A:MG802 3.9 20.8 1.0 CG A:HIS563 4.1 24.9 1.0 CD2 A:HIS525 4.1 20.8 1.0 ND1 A:HIS563 4.1 24.8 1.0 CB A:ASP674 4.3 22.1 1.0 CB A:ASP564 4.3 24.6 1.0 CG A:HIS529 4.5 15.9 1.0 NE2 A:HIS525 4.5 20.8 1.0 ND1 A:HIS529 4.6 15.7 1.0 CG2 A:VAL533 4.6 18.4 1.0 CA A:ASP674 4.8 22.3 1.0 O A:HOH907 4.8 35.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:34.6 occ:1.00 O B:HOH918 2.1 37.3 1.0 O B:HOH921 2.1 9.7 1.0 OD2 B:ASP564 2.1 19.1 1.0 NE2 B:HIS563 2.1 18.5 1.0 OD1 B:ASP674 2.2 20.6 1.0 NE2 B:HIS529 2.2 21.4 1.0 CD2 B:HIS563 2.9 18.6 1.0 CE1 B:HIS529 2.9 21.3 1.0 CG B:ASP564 3.1 19.5 1.0 CG B:ASP674 3.2 20.8 1.0 CE1 B:HIS563 3.2 18.5 1.0 CD2 B:HIS529 3.3 21.2 1.0 OD1 B:ASP564 3.5 19.1 1.0 MG B:MG802 3.6 14.5 1.0 OD2 B:ASP674 3.7 20.9 1.0 O B:HOH917 3.7 10.4 1.0 ND1 B:HIS529 4.1 21.2 1.0 CG B:HIS563 4.1 18.7 1.0 CD2 B:HIS525 4.2 25.2 1.0 ND1 B:HIS563 4.2 18.7 1.0 CB B:ASP564 4.3 19.7 1.0 CG B:HIS529 4.3 21.1 1.0 O B:HOH906 4.5 25.3 1.0 CB B:ASP674 4.5 20.8 1.0 NE2 B:HIS525 4.6 25.0 1.0 O B:HOH909 4.8 12.2 1.0 CA B:ASP674 4.8 20.2 1.0 CG2 B:VAL533 4.9 22.9 1.0 O B:ASP674 4.9 21.1 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