Magnesium in PDB 6ind: 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: 6ind 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)	40.68 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.835, 80.185, 163.334, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.9

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 6ind). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6ind:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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:14.2 occ:1.00 O A:HOH620 2.0 14.2 1.0 OD1 A:ASP201 2.1 14.7 1.0 O A:HOH685 2.1 15.0 1.0 O A:HOH726 2.2 14.9 1.0 O A:HOH661 2.2 16.4 1.0 O A:HOH650 2.2 15.0 1.0 CG A:ASP201 3.1 15.4 1.0 OD2 A:ASP201 3.4 14.6 1.0 ZN A:ZN503 3.7 21.1 1.0 O A:HOH763 3.9 23.6 1.0 O A:HOH716 4.1 18.5 1.0 OE2 A:GLU230 4.1 19.2 1.0 CD2 A:HIS200 4.1 14.9 1.0 NE2 A:HIS233 4.1 16.3 1.0 O A:HIS200 4.1 15.5 1.0 OG1 A:THR271 4.3 14.6 1.0 CD2 A:HIS233 4.3 12.3 1.0 O A:HOH706 4.4 21.1 1.0 OD2 A:ASP318 4.4 20.3 1.0 CD2 A:HIS204 4.4 17.7 1.0 CB A:ASP201 4.4 15.8 1.0 NE2 A:HIS200 4.5 12.8 1.0 O A:THR271 4.6 17.2 1.0 NE2 A:HIS204 4.8 19.2 1.0 CB A:THR271 4.8 16.6 1.0 CA A:ASP201 4.8 13.7 1.0 CD2 A:HIS160 4.8 18.1 1.0 CG A:GLU230 4.8 16.6 1.0 CD A:GLU230 4.9 18.2 1.0 NE2 A:HIS160 4.9 17.7 1.0 C A:HIS200 5.0 15.6 1.0

Magnesium binding site 2 out of 3 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:Mg503 b:32.0 occ:1.00 O B:HOH627 2.2 27.7 1.0 O B:HOH602 2.2 31.2 1.0 OD1 B:ASP301 2.3 29.3 1.0 CG B:ASP301 3.2 28.3 1.0 OD2 B:ASP301 3.6 28.7 1.0 O B:ASP301 3.8 39.6 1.0 CB B:ASP301 4.5 36.2 1.0 C B:ASP301 4.6 38.7 1.0 CA B:ASP301 4.6 35.9 1.0

Magnesium binding site 3 out of 3 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 3 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:18.9 occ:1.00 O B:HOH606 2.0 18.2 1.0 O B:HOH684 2.0 17.8 1.0 OD1 B:ASP201 2.2 25.1 1.0 O B:HOH607 2.2 14.4 1.0 O B:HOH642 2.2 16.2 1.0 O B:HOH613 2.2 19.2 1.0 CG B:ASP201 3.1 22.3 1.0 OD2 B:ASP201 3.4 16.7 1.0 ZN B:ZN505 3.7 26.4 1.0 O B:HOH692 3.8 35.1 1.0 OE2 B:GLU230 4.0 20.2 1.0 O B:HOH655 4.0 23.4 1.0 CD2 B:HIS200 4.2 19.3 1.0 O B:HIS200 4.2 18.4 1.0 NE2 B:HIS233 4.2 20.1 1.0 O B:HOH677 4.2 23.5 1.0 OG1 B:THR271 4.3 17.0 1.0 CD2 B:HIS233 4.4 18.3 1.0 OD2 B:ASP318 4.4 26.8 1.0 CB B:ASP201 4.5 19.0 1.0 CD2 B:HIS204 4.6 20.4 1.0 O B:THR271 4.6 20.3 1.0 NE2 B:HIS200 4.6 19.0 1.0 CG B:GLU230 4.7 16.4 1.0 CB B:THR271 4.7 18.7 1.0 CD B:GLU230 4.8 20.2 1.0 CD2 B:HIS160 4.8 19.6 1.0 NE2 B:HIS204 4.8 20.0 1.0 CA B:ASP201 4.9 18.0 1.0 NE2 B:HIS160 4.9 21.4 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