Magnesium in PDB 8w4q: Crystal Structure of PDE4D Complexed with Cx-4945

All present enzymatic activity of Crystal Structure of PDE4D Complexed with Cx-4945:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with Cx-4945, PDB code: 8w4q 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)	28.32 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.509, 79.99, 162.723, 90, 90, 90
R / Rfree (%)	22.6 / 24

The structure of Crystal Structure of PDE4D Complexed with Cx-4945 also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Complexed with Cx-4945 (pdb code 8w4q). 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 Cx-4945, PDB code: 8w4q:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with Cx-4945


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 Cx-4945 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:20.0 occ:1.00 O A:HOH622 2.0 18.9 1.0 OD1 A:ASP201 2.1 32.4 1.0 O A:HOH625 2.1 20.4 1.0 O A:HOH640 2.1 21.6 1.0 O A:HOH621 2.1 20.8 1.0 O A:HOH602 2.2 20.8 1.0 CG A:ASP201 3.1 31.1 1.0 OD2 A:ASP201 3.4 33.9 1.0 ZN A:ZN502 3.8 20.4 1.0 OE2 A:GLU230 4.0 21.2 1.0 NE2 A:HIS233 4.1 19.7 1.0 CD2 A:HIS200 4.1 26.5 1.0 O A:HOH615 4.1 24.2 1.0 O A:HIS200 4.1 17.8 1.0 OG1 A:THR271 4.2 21.8 1.0 O A:HOH651 4.3 30.2 1.0 CD2 A:HIS233 4.3 18.8 1.0 CB A:ASP201 4.4 27.2 1.0 O A:HOH601 4.5 41.3 1.0 CD2 A:HIS204 4.5 22.1 1.0 OD2 A:ASP318 4.5 26.3 1.0 NE2 A:HIS200 4.5 28.7 1.0 O24 A:3NG503 4.6 40.4 1.0 O A:THR271 4.7 25.4 1.0 CD2 A:HIS160 4.7 22.0 1.0 CA A:ASP201 4.8 21.8 1.0 CB A:THR271 4.8 22.8 1.0 NE2 A:HIS204 4.9 22.9 1.0 CG A:GLU230 4.9 19.6 1.0 CD A:GLU230 4.9 20.6 1.0 NE2 A:HIS160 4.9 21.9 1.0 C A:HIS200 5.0 18.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with Cx-4945


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 Cx-4945 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:23.1 occ:1.00 OD1 B:ASP201 1.9 41.6 1.0 O B:HOH615 2.0 23.7 1.0 O B:HOH621 2.0 23.1 1.0 O B:HOH605 2.0 25.3 1.0 O B:HOH608 2.1 23.9 1.0 O B:HOH618 2.2 25.2 1.0 CG B:ASP201 3.0 40.8 1.0 OD2 B:ASP201 3.4 45.1 1.0 ZN B:ZN502 3.8 27.0 1.0 OE2 B:GLU230 4.1 26.2 1.0 O B:HIS200 4.1 24.8 1.0 NE2 B:HIS233 4.1 23.6 1.0 CD2 B:HIS200 4.1 26.8 1.0 O B:HOH602 4.2 25.8 1.0 OG1 B:THR271 4.3 28.0 1.0 CD2 B:HIS233 4.3 23.9 1.0 CB B:ASP201 4.4 36.5 1.0 O B:HOH635 4.4 31.5 1.0 OD2 B:ASP318 4.4 47.0 1.0 O25 B:3NG503 4.5 44.7 1.0 CD2 B:HIS204 4.5 23.2 1.0 NE2 B:HIS200 4.5 27.4 1.0 CA B:ASP201 4.7 29.7 1.0 CD2 B:HIS160 4.7 29.2 1.0 O B:THR271 4.8 29.1 1.0 NE2 B:HIS204 4.8 23.1 1.0 C B:HIS200 4.9 26.0 1.0 CB B:THR271 4.9 30.1 1.0 CG B:GLU230 4.9 26.2 1.0 CD B:GLU230 4.9 26.1 1.0 NE2 B:HIS160 5.0 28.1 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