Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 1, PDB code: 6kjz:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502 b:15.4 occ:1.00 O A:HOH635 2.1 19.8 1.0 O A:HOH689 2.1 19.9 1.0 OD1 A:ASP201 2.1 20.1 1.0 O A:HOH659 2.1 16.2 1.0 O A:HOH636 2.2 19.2 1.0 O A:HOH648 2.2 22.4 1.0 CG A:ASP201 3.1 19.4 1.0 OD2 A:ASP201 3.3 20.1 1.0 ZN A:ZN501 3.7 25.2 1.0 O A:HOH693 4.1 12.5 1.0 O A:HOH704 4.1 21.3 1.0 OE2 A:GLU230 4.1 22.5 1.0 CD2 A:HIS200 4.2 15.7 1.0 NE2 A:HIS233 4.2 20.1 1.0 O A:HIS200 4.2 19.5 1.0 CD2 A:HIS233 4.4 18.3 1.0 CD2 A:HIS204 4.4 17.9 1.0 CB A:ASP201 4.5 19.3 1.0 NE2 A:HIS200 4.5 18.9 1.0 OD2 A:ASP318 4.5 18.6 1.0 OG1 A:THR271 4.5 18.7 1.0 O A:HOH679 4.6 27.5 1.0 NE2 A:HIS160 4.6 20.2 1.0 CD2 A:HIS160 4.6 21.9 1.0 NE2 A:HIS204 4.6 17.3 1.0 CG A:GLU230 4.8 20.9 1.0 CA A:ASP201 4.9 18.2 1.0 CD A:GLU230 4.9 23.2 1.0 CB A:THR271 4.9 21.5 1.0 O A:THR271 5.0 22.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502 b:16.7 occ:1.00 O B:HOH639 1.9 18.9 1.0 O B:HOH612 2.0 18.1 1.0 OD1 B:ASP201 2.0 19.0 1.0 O B:HOH614 2.1 21.2 1.0 O B:HOH652 2.2 20.0 1.0 O B:HOH670 2.2 16.0 1.0 CG B:ASP201 3.0 18.6 1.0 OD2 B:ASP201 3.3 19.3 1.0 ZN B:ZN501 3.5 31.4 1.0 O B:HIS200 3.9 21.1 1.0 CD2 B:HIS200 3.9 21.4 1.0 OE2 B:GLU230 4.0 21.2 1.0 O B:HOH634 4.1 20.9 1.0 O B:HOH645 4.1 21.7 1.0 OG1 B:THR271 4.2 22.0 1.0 NE2 B:HIS233 4.3 21.4 1.0 NE2 B:HIS200 4.3 23.2 1.0 CB B:ASP201 4.4 20.5 1.0 CD2 B:HIS233 4.4 22.7 1.0 OD1 B:ASP318 4.5 26.6 1.0 CB B:THR271 4.7 20.0 1.0 CD2 B:HIS204 4.8 21.0 1.0 NE2 B:HIS160 4.8 19.9 1.0 CA B:ASP201 4.8 23.7 1.0 C B:HIS200 4.8 21.4 1.0 OD2 B:ASP318 4.9 23.0 1.0 O B:THR271 4.9 23.7 1.0 CD2 B:HIS160 4.9 19.1 1.0 CD B:GLU230 4.9 20.9 1.0 CG B:GLU230 4.9 17.9 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