Magnesium in PDB 6inm: Crystal Structure of PDE4D Complexed with A Novel Inhibitor

All present enzymatic activity of Crystal Structure of PDE4D Complexed with A Novel Inhibitor:
3.1.4.53;

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6inm was solved by X.L.Zhang, H.X.Su, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.01 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.122, 80.104, 163.259, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The structure of Crystal Structure of PDE4D Complexed with A Novel Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor (pdb code 6inm). 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 A Novel Inhibitor, PDB code: 6inm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


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 A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:18.0 occ:1.00 O A:HOH618 2.0 18.2 1.0 O A:HOH714 2.0 19.3 1.0 OD1 A:ASP201 2.1 21.6 1.0 O A:HOH663 2.2 18.2 1.0 O A:HOH681 2.2 17.6 1.0 O A:HOH632 2.3 21.1 1.0 CG A:ASP201 3.0 22.8 1.0 OD2 A:ASP201 3.3 21.8 1.0 ZN A:ZN501 3.6 23.9 1.0 O A:HOH691 3.9 18.5 1.0 O A:HOH727 4.0 46.7 1.0 CD2 A:HIS200 4.1 16.8 1.0 OE2 A:GLU230 4.1 24.3 1.0 O A:HIS200 4.1 19.7 1.0 NE2 A:HIS233 4.1 19.2 1.0 O A:HOH709 4.2 25.3 1.0 CD2 A:HIS233 4.4 17.9 1.0 OG1 A:THR271 4.4 22.2 1.0 CD2 A:HIS204 4.4 16.1 1.0 CB A:ASP201 4.4 21.3 1.0 OD2 A:ASP318 4.4 24.7 1.0 NE2 A:HIS200 4.5 17.5 1.0 CD2 A:HIS160 4.7 17.5 1.0 O A:THR271 4.7 26.1 1.0 NE2 A:HIS204 4.7 19.4 1.0 CA A:ASP201 4.8 18.0 1.0 NE2 A:HIS160 4.8 18.6 1.0 CB A:THR271 4.8 25.1 1.0 CG A:GLU230 4.9 20.3 1.0 CD A:GLU230 4.9 26.8 1.0 C A:HIS200 5.0 20.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor


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 A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:22.2 occ:1.00 O B:HOH611 2.0 22.7 1.0 OD1 B:ASP201 2.0 25.7 1.0 O B:HOH610 2.0 20.6 1.0 O B:HOH620 2.1 20.6 1.0 O B:HOH660 2.2 23.2 1.0 O B:HOH622 2.3 22.1 1.0 CG B:ASP201 3.1 25.6 1.0 OD2 B:ASP201 3.4 26.1 1.0 ZN B:ZN501 3.7 29.4 1.0 O B:HOH657 3.9 26.0 1.0 OE2 B:GLU230 3.9 26.5 1.0 O B:HOH650 4.0 43.9 1.0 O B:HIS200 4.0 21.5 1.0 CD2 B:HIS200 4.1 19.7 1.0 NE2 B:HIS233 4.1 23.0 1.0 OG1 B:THR271 4.2 24.3 1.0 O B:HOH652 4.2 26.1 1.0 CD2 B:HIS233 4.3 23.0 1.0 OD1 B:ASP318 4.4 37.0 1.0 CB B:ASP201 4.4 22.5 1.0 NE2 B:HIS200 4.5 19.3 1.0 CD2 B:HIS204 4.6 19.9 1.0 O B:THR271 4.6 27.2 1.0 CA B:ASP201 4.7 23.1 1.0 CB B:THR271 4.8 25.4 1.0 O B:HOH631 4.8 43.1 1.0 NE2 B:HIS204 4.8 19.8 1.0 CD2 B:HIS160 4.8 22.0 1.0 CD B:GLU230 4.8 25.1 1.0 CG B:GLU230 4.9 22.5 1.0 C B:HIS200 4.9 23.0 1.0 NE2 B:HIS160 4.9 20.5 1.0

X.Zhang, G.Dong, H.Li, W.Chen, J.Li, C.Feng, Z.Gu, F.Zhu, R.Zhang, M.Li, W.Tang, H.Liu, Y.Xu. Structure-Aided Identification and Optimization of Tetrahydro-Isoquinolines As Novel PDE4 Inhibitors Leading to Discovery of An Effective Antipsoriasis Agent. J.Med.Chem. V. 62 5579 2019.
ISSN: ISSN 0022-2623
PubMed: 31099559
DOI: 10.1021/ACS.JMEDCHEM.9B00518