Magnesium in PDB 6ink: 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: 6ink 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)	46.92 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.817, 80.276, 163.321, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.2

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 6ink). 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: 6ink:
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:18.3 occ:1.00 O A:HOH614 2.1 16.9 1.0 OD1 A:ASP201 2.1 18.0 1.0 O A:HOH664 2.1 18.3 1.0 O A:HOH669 2.1 17.1 1.0 O A:HOH630 2.2 16.7 1.0 O A:HOH704 2.2 17.4 1.0 CG A:ASP201 3.1 18.0 1.0 OD2 A:ASP201 3.4 15.4 1.0 ZN A:ZN501 3.8 21.8 1.0 O A:HOH742 4.0 48.5 1.0 OE2 A:GLU230 4.1 22.6 1.0 O A:HOH692 4.1 18.6 1.0 NE2 A:HIS233 4.1 18.4 1.0 CD2 A:HIS200 4.1 19.1 1.0 O A:HIS200 4.2 17.1 1.0 OG1 A:THR271 4.3 20.6 1.0 CD2 A:HIS233 4.3 15.2 1.0 O A:HOH696 4.4 26.0 1.0 OD2 A:ASP318 4.5 24.9 1.0 CD2 A:HIS204 4.5 16.2 1.0 CB A:ASP201 4.5 17.4 1.0 NE2 A:HIS200 4.6 17.0 1.0 O A:THR271 4.6 20.0 1.0 CB A:THR271 4.8 22.6 1.0 NE2 A:HIS204 4.8 20.9 1.0 CA A:ASP201 4.8 15.3 1.0 CG A:GLU230 4.8 21.5 1.0 CD2 A:HIS160 4.8 19.0 1.0 NE2 A:HIS160 4.9 19.4 1.0 CD A:GLU230 4.9 25.8 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:20.2 occ:1.00 OD1 B:ASP201 2.1 20.9 1.0 O B:HOH607 2.1 19.8 1.0 O B:HOH612 2.1 19.3 1.0 O B:HOH669 2.1 21.4 1.0 O B:HOH635 2.2 21.8 1.0 O B:HOH638 2.2 19.5 1.0 CG B:ASP201 3.1 22.3 1.0 OD2 B:ASP201 3.4 21.2 1.0 ZN B:ZN501 3.8 26.4 1.0 OE2 B:GLU230 4.0 25.0 1.0 O B:HOH687 4.1 45.8 1.0 CD2 B:HIS200 4.1 20.7 1.0 NE2 B:HIS233 4.1 20.5 1.0 O B:HIS200 4.1 21.7 1.0 O B:HOH658 4.1 21.8 1.0 OG1 B:THR271 4.3 22.9 1.0 O B:HOH663 4.3 27.6 1.0 CD2 B:HIS233 4.3 18.2 1.0 OD2 B:ASP318 4.4 34.0 1.0 CB B:ASP201 4.5 20.8 1.0 CD2 B:HIS204 4.5 20.3 1.0 NE2 B:HIS200 4.6 22.0 1.0 O B:THR271 4.6 26.4 1.0 CD2 B:HIS160 4.8 21.7 1.0 CA B:ASP201 4.8 19.4 1.0 NE2 B:HIS204 4.8 20.8 1.0 CG B:GLU230 4.8 19.4 1.0 CB B:THR271 4.8 24.3 1.0 CD B:GLU230 4.9 23.8 1.0 NE2 B:HIS160 4.9 21.4 1.0 C B:HIS200 5.0 20.9 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