Magnesium in PDB 7f2k: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A, PDB code: 7f2k 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)	23.58 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.063, 80.697, 163.385, 90, 90, 90
R / Rfree (%)	20.8 / 25.7

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A (pdb code 7f2k). 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 PDE4D Catalytic Domain Complexed with Compound 17A, PDB code: 7f2k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A


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 PDE4D Catalytic Domain Complexed with Compound 17A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:11.4 occ:1.00 O A:HOH774 1.9 11.3 1.0 O A:HOH701 2.0 11.7 1.0 OD1 A:ASP201 2.1 9.2 1.0 O A:HOH788 2.1 13.6 1.0 O A:HOH750 2.2 10.5 1.0 O A:HOH765 2.3 12.4 1.0 CG A:ASP201 3.1 13.5 1.0 O35 A:0X8603 3.2 31.7 1.0 OD2 A:ASP201 3.4 10.2 1.0 ZN A:ZN601 3.8 22.4 1.0 OE2 A:GLU230 4.1 15.6 1.0 CD2 A:HIS200 4.1 10.0 1.0 C34 A:0X8603 4.1 23.9 1.0 O A:HIS200 4.2 12.7 1.0 NE2 A:HIS233 4.2 13.3 1.0 OG1 A:THR271 4.2 14.5 1.0 O A:HOH785 4.3 13.2 1.0 CD2 A:HIS233 4.4 11.2 1.0 O36 A:0X8603 4.4 18.3 1.0 CB A:ASP201 4.4 9.3 1.0 CD2 A:HIS204 4.5 9.1 1.0 NE2 A:HIS200 4.6 11.1 1.0 OD2 A:ASP318 4.6 18.7 1.0 CA A:ASP201 4.8 9.1 1.0 O A:THR271 4.8 17.0 1.0 NE2 A:HIS204 4.9 14.1 1.0 CD2 A:HIS160 4.9 15.0 1.0 CB A:THR271 4.9 18.1 1.0 CD A:GLU230 5.0 16.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A


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 PDE4D Catalytic Domain Complexed with Compound 17A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:14.2 occ:1.00 O B:HOH701 2.0 14.3 1.0 OD1 B:ASP201 2.0 13.4 1.0 O B:HOH711 2.1 13.0 1.0 O B:HOH742 2.1 15.8 1.0 O B:HOH739 2.2 14.9 1.0 O B:HOH749 2.2 14.5 1.0 CG B:ASP201 3.1 15.1 1.0 O35 B:0X8603 3.4 31.9 1.0 OD2 B:ASP201 3.4 10.8 1.0 ZN B:ZN601 3.6 21.9 1.0 O B:HIS200 3.9 14.2 1.0 CD2 B:HIS200 4.1 16.2 1.0 OG1 B:THR271 4.1 13.6 1.0 NE2 B:HIS233 4.2 14.2 1.0 OE2 B:GLU230 4.2 16.8 1.0 C34 B:0X8603 4.2 22.7 1.0 CD2 B:HIS233 4.3 13.6 1.0 CB B:ASP201 4.4 13.5 1.0 O B:HOH751 4.5 20.0 1.0 O36 B:0X8603 4.5 16.2 1.0 O B:HOH768 4.6 28.2 1.0 NE2 B:HIS200 4.6 14.7 1.0 CD2 B:HIS204 4.6 13.8 1.0 OD2 B:ASP318 4.7 22.8 1.0 CD2 B:HIS160 4.8 14.0 1.0 CA B:ASP201 4.8 14.6 1.0 CB B:THR271 4.8 17.6 1.0 C B:HIS200 4.8 16.1 1.0 O B:THR271 4.9 21.0 1.0 CG B:GLU230 4.9 16.1 1.0 CD B:GLU230 5.0 18.0 1.0 NE2 B:HIS204 5.0 15.9 1.0 OD1 B:ASP318 5.0 16.4 1.0

Y.Y.Huang, J.Deng, Y.J.Tian, J.Liang, X.Xie, Y.Huang, J.Zhu, Z.Zhu, Q.Zhou, X.He, H.B.Luo. Mangostanin Derivatives As Novel and Orally Active Phosphodiesterase 4 Inhibitors For the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem. V. 64 13736 2021.
ISSN: ISSN 0022-2623
PubMed: 34520193
DOI: 10.1021/ACS.JMEDCHEM.1C01085