Magnesium in PDB 6kk0: Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E

All present enzymatic activity of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E:
3.1.4.53;

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E, PDB code: 6kk0 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)	21.93 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.365, 77.984, 163.344, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.7

The structure of Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E 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 4E (pdb code 6kk0). 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 4E, PDB code: 6kk0:
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 4E


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.4 occ:1.00 O A:HOH657 1.8 49.8 1.0 OD1 A:ASP201 2.0 16.7 1.0 O A:HOH663 2.2 18.7 1.0 O A:HOH659 2.2 16.3 1.0 O A:HOH702 2.3 20.8 1.0 O A:HOH655 2.3 15.8 1.0 CG A:ASP201 3.0 16.6 1.0 OD2 A:ASP201 3.2 17.2 1.0 ZN A:ZN502 3.5 23.5 1.0 O37 A:M36501 3.9 21.8 1.0 CD2 A:HIS200 4.0 18.1 1.0 O A:HIS200 4.0 16.2 1.0 NE2 A:HIS233 4.2 15.6 1.0 OE2 A:GLU230 4.2 13.7 1.0 O A:HOH716 4.3 20.1 1.0 OG1 A:THR271 4.3 16.1 1.0 CB A:ASP201 4.4 19.6 1.0 OD2 A:ASP318 4.4 24.2 1.0 NE2 A:HIS200 4.5 12.4 1.0 C35 A:M36501 4.5 23.0 1.0 CD2 A:HIS233 4.5 15.3 1.0 O36 A:M36501 4.5 23.9 1.0 CD2 A:HIS204 4.7 17.5 1.0 O A:THR271 4.7 13.8 1.0 CD2 A:HIS160 4.7 15.0 1.0 CB A:THR271 4.8 13.7 1.0 CA A:ASP201 4.8 12.3 1.0 O A:HOH734 4.8 26.4 1.0 C A:HIS200 4.9 14.9 1.0 CG A:GLU230 4.9 14.5 1.0 NE2 A:HIS160 5.0 17.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Strucure of PDE4D Catalytic Domain Complexed with Compound 4E


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 4E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:14.5 occ:1.00 O B:HOH641 1.9 18.2 1.0 O B:HOH622 2.0 14.0 1.0 O B:HOH633 2.1 16.5 1.0 OD1 B:ASP201 2.2 16.6 1.0 O B:HOH673 2.2 12.7 1.0 O B:HOH672 2.2 16.2 1.0 CG B:ASP201 3.1 25.7 1.0 OD2 B:ASP201 3.4 17.7 1.0 ZN B:ZN502 3.7 22.5 1.0 OE2 B:GLU230 4.0 12.9 1.0 CD2 B:HIS200 4.0 16.4 1.0 O B:HOH680 4.1 20.4 1.0 O37 B:M36501 4.1 21.6 1.0 O B:HIS200 4.1 19.2 1.0 OG1 B:THR271 4.2 15.7 1.0 NE2 B:HIS233 4.3 18.5 1.0 OD2 B:ASP318 4.4 25.7 1.0 CD2 B:HIS233 4.5 19.1 1.0 NE2 B:HIS200 4.5 19.2 1.0 CB B:ASP201 4.5 17.8 1.0 O B:HOH613 4.5 20.1 1.0 O B:THR271 4.6 17.2 1.0 O36 B:M36501 4.7 26.3 1.0 C35 B:M36501 4.7 22.6 1.0 CD2 B:HIS204 4.7 13.1 1.0 CG B:GLU230 4.8 15.1 1.0 CD B:GLU230 4.8 17.1 1.0 CB B:THR271 4.8 20.5 1.0 CD2 B:HIS160 4.8 19.4 1.0 CA B:ASP201 4.9 16.5 1.0 C B:HIS200 5.0 19.1 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