Zinc in PDB 6kjz: Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1

All present enzymatic activity of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1:
3.1.4.53;

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1, PDB code: 6kjz was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.15 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.311, 79.700, 163.316, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.6

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1 (pdb code 6kjz). 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 Strucure of PDE4D Catalytic Domain Complexed with Compound 1, PDB code: 6kjz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:25.2 occ:1.00 O A:HOH693 2.1 12.5 1.0 NE2 A:HIS200 2.1 18.9 1.0 OD1 A:ASP318 2.2 18.6 1.0 O A:HOH635 2.2 19.8 1.0 NE2 A:HIS164 2.2 17.3 1.0 OD2 A:ASP201 2.2 20.1 1.0 CG A:ASP318 3.0 17.1 1.0 CD2 A:HIS200 3.1 15.7 1.0 CE1 A:HIS164 3.2 19.2 1.0 CE1 A:HIS200 3.2 15.8 1.0 OD2 A:ASP318 3.2 18.6 1.0 CG A:ASP201 3.2 19.4 1.0 CD2 A:HIS164 3.2 15.3 1.0 OD1 A:ASP201 3.7 20.1 1.0 MG A:MG502 3.7 15.4 1.0 O A:HOH689 4.0 19.9 1.0 O A:HOH649 4.1 26.6 1.0 CD2 A:HIS160 4.2 21.9 1.0 CG A:HIS200 4.2 16.8 1.0 ND1 A:HIS200 4.3 17.2 1.0 ND1 A:HIS164 4.3 18.3 1.0 CB A:ASP201 4.3 19.3 1.0 CB A:ASP318 4.3 20.5 1.0 CG A:HIS164 4.4 18.7 1.0 NE2 A:HIS160 4.5 20.2 1.0 O A:HOH648 4.6 22.4 1.0 CG2 A:VAL168 4.7 16.6 1.0 CA A:ASP318 4.9 16.2 1.0

Zinc binding site 2 out of 2 in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:31.4 occ:1.00 OD2 B:ASP318 2.0 23.0 1.0 O B:HOH639 2.1 18.9 1.0 OD2 B:ASP201 2.1 19.3 1.0 NE2 B:HIS200 2.2 23.2 1.0 NE2 B:HIS164 2.3 23.3 1.0 O B:HOH634 2.4 20.9 1.0 CG B:ASP318 3.0 26.7 1.0 CD2 B:HIS200 3.0 21.4 1.0 CE1 B:HIS164 3.1 21.0 1.0 CG B:ASP201 3.1 18.6 1.0 CE1 B:HIS200 3.3 23.2 1.0 OD1 B:ASP318 3.3 26.6 1.0 CD2 B:HIS164 3.3 22.0 1.0 MG B:MG502 3.5 16.7 1.0 OD1 B:ASP201 3.6 19.0 1.0 O B:HOH670 3.8 16.0 1.0 CD2 B:HIS160 4.1 19.1 1.0 O B:HOH632 4.2 28.0 1.0 CG B:HIS200 4.2 25.3 1.0 NE2 B:HIS160 4.2 19.9 1.0 ND1 B:HIS164 4.3 23.8 1.0 CB B:ASP318 4.3 22.5 1.0 ND1 B:HIS200 4.3 22.7 1.0 CG B:HIS164 4.4 21.0 1.0 CB B:ASP201 4.4 20.5 1.0 O B:HOH612 4.6 18.1 1.0 CG2 B:VAL168 4.8 28.8 1.0 CA B:ASP318 4.9 25.8 1.0 O B:HOH614 5.0 21.2 1.0

J.Liang, Y.Y.Huang, Q.Zhou, Y.Gao, Z.Li, D.Wu, S.Yu, L.Guo, Z.Chen, L.Huang, S.H.Liang, X.He, R.Wu, H.B.Luo. Discovery and Optimization of Alpha-Mangostin Derivatives As Novel PDE4 Inhibitors For the Treatment of Vascular Dementia. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32115956
DOI: 10.1021/ACS.JMEDCHEM.0C00060