Magnesium in PDB 8w4r: Crystal Structure of PDE4D Complexed with Cvt-313

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Cvt-313:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Cvt-313, PDB code: 8w4r was solved by J.Y.Liu, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.33 / 1.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.63, 80.71, 163.67, 90, 90, 90
R / Rfree (%)	20.7 / 21.5

The structure of Crystal Structure of PDE4D Complexed with Cvt-313 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Complexed with Cvt-313 (pdb code 8w4r). 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 Complexed with Cvt-313, PDB code: 8w4r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with Cvt-313


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 Complexed with Cvt-313 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.9 occ:1.00 OD1 A:ASP201 2.0 16.9 1.0 O A:HOH662 2.1 17.3 1.0 O A:HOH629 2.1 19.6 1.0 O A:HOH619 2.1 17.9 1.0 O A:HOH694 2.1 19.4 1.0 O A:HOH602 2.1 17.7 1.0 CG A:ASP201 3.1 17.2 1.0 OD2 A:ASP201 3.4 16.1 1.0 ZN A:ZN503 3.8 20.3 1.0 OE2 A:GLU230 4.1 21.6 1.0 O A:HOH669 4.1 19.0 1.0 NE2 A:HIS233 4.1 15.8 1.0 CD2 A:HIS200 4.2 16.4 1.0 O A:HIS200 4.2 14.9 1.0 OG1 A:THR271 4.2 17.2 1.0 O A:HOH680 4.3 23.8 1.0 CD2 A:HIS233 4.4 16.7 1.0 CB A:ASP201 4.4 15.1 1.0 OD1 A:ASP318 4.4 23.6 1.0 CD2 A:HIS204 4.5 17.8 1.0 NE2 A:HIS200 4.6 16.8 1.0 O A:THR271 4.7 20.3 1.0 NE2 A:HIS160 4.7 18.5 1.0 CB A:THR271 4.8 20.4 1.0 CA A:ASP201 4.8 15.4 1.0 CG A:GLU230 4.8 18.9 1.0 CD2 A:HIS160 4.8 17.3 1.0 NE2 A:HIS204 4.8 18.5 1.0 CD A:GLU230 4.9 20.6 1.0 C A:HIS200 5.0 16.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Cvt-313


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 Complexed with Cvt-313 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:18.6 occ:1.00 OD1 B:ASP201 2.1 19.4 1.0 O B:HOH642 2.1 18.7 1.0 O B:HOH621 2.1 19.4 1.0 O B:HOH661 2.1 20.1 1.0 O B:HOH613 2.2 18.2 1.0 O B:HOH601 2.2 19.9 1.0 CG B:ASP201 3.1 18.0 1.0 OD2 B:ASP201 3.5 18.4 1.0 ZN B:ZN503 3.8 23.1 1.0 OE2 B:GLU230 4.0 22.6 1.0 O B:HOH648 4.1 22.1 1.0 O B:HIS200 4.1 19.4 1.0 NE2 B:HIS233 4.1 18.1 1.0 CD2 B:HIS200 4.2 18.6 1.0 O B:HOH658 4.2 23.1 1.0 OG1 B:THR271 4.3 19.8 1.0 CD2 B:HIS233 4.4 16.5 1.0 CB B:ASP201 4.5 18.3 1.0 OD2 B:ASP318 4.5 26.9 1.0 CD2 B:HIS204 4.6 17.6 1.0 NE2 B:HIS200 4.6 19.2 1.0 O B:THR271 4.7 22.6 1.0 NE2 B:HIS160 4.8 21.7 1.0 CA B:ASP201 4.8 18.2 1.0 CD2 B:HIS160 4.8 18.5 1.0 NE2 B:HIS204 4.8 19.8 1.0 CB B:THR271 4.8 19.9 1.0 CG B:GLU230 4.8 19.8 1.0 CD B:GLU230 4.8 20.5 1.0 C B:HIS200 5.0 18.0 1.0

J.Liu, X.Zhang, G.Chen, Q.Shao, Y.Zou, Z.Li, H.Su, M.Li, Y.Xu. Drug Repurposing and Structure-Based Discovery of New PDE4 and PDE5 Inhibitors. Eur.J.Med.Chem. V. 262 15893 2023.
ISSN: ISSN 0223-5234
PubMed: 37918035
DOI: 10.1016/J.EJMECH.2023.115893