Magnesium in PDB 6imo: 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: 6imo 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)	29.27 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.547, 80.477, 163.861, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.5

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 6imo). 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: 6imo:
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:6.2 occ:1.00 OD1 A:ASP201 2.1 5.8 1.0 O A:HOH775 2.1 7.3 1.0 O A:HOH664 2.1 6.2 1.0 O A:HOH696 2.1 7.7 1.0 O A:HOH694 2.1 7.2 1.0 O A:HOH611 2.1 7.2 1.0 CG A:ASP201 3.1 5.4 1.0 OD2 A:ASP201 3.4 5.1 1.0 ZN A:ZN501 3.7 9.9 1.0 O A:HOH803 3.9 22.2 1.0 OE2 A:GLU230 4.0 10.0 1.0 NE2 A:HIS233 4.1 6.3 1.0 O A:HOH732 4.1 7.3 1.0 CD2 A:HIS200 4.2 4.0 1.0 O A:HIS200 4.2 5.7 1.0 OG1 A:THR271 4.3 7.5 1.0 O A:HOH719 4.3 13.3 1.0 CD2 A:HIS233 4.4 6.1 1.0 CB A:ASP201 4.4 5.8 1.0 OD2 A:ASP318 4.5 13.1 1.0 NE2 A:HIS200 4.5 4.5 1.0 CD2 A:HIS204 4.5 6.9 1.0 O A:HOH649 4.6 24.5 1.0 O A:THR271 4.7 10.1 1.0 CB A:THR271 4.8 8.4 1.0 NE2 A:HIS160 4.8 10.6 1.0 CA A:ASP201 4.8 5.8 1.0 CD2 A:HIS160 4.8 7.5 1.0 CG A:GLU230 4.8 8.5 1.0 NE2 A:HIS204 4.9 7.5 1.0 CD A:GLU230 4.9 8.9 1.0 C A:HIS200 5.0 5.6 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 A:Mg503 b:15.0 occ:1.00 O A:ASP151 2.0 10.2 1.0 O A:HOH729 2.1 14.8 1.0 O A:TYR153 2.2 10.5 1.0 C A:ASP151 3.1 12.0 1.0 C A:TYR153 3.3 10.7 1.0 CA A:HIS154 4.0 9.6 1.0 CA A:ASP151 4.0 12.5 1.0 N A:TYR153 4.0 8.4 1.0 N A:HIS152 4.0 9.3 1.0 N A:HIS154 4.1 9.3 1.0 N A:ALA155 4.1 15.1 1.0 C A:HIS152 4.1 8.7 1.0 CA A:HIS152 4.2 9.3 1.0 O A:HOH669 4.3 14.6 1.0 CA A:TYR153 4.3 8.3 1.0 O A:GLU150 4.5 9.0 1.0 C A:HIS154 4.5 12.7 1.0 O A:HOH690 4.6 15.6 1.0 O A:HIS152 4.8 8.7 1.0 CB A:ASP151 4.8 10.4 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:Mg502 b:7.4 occ:1.00 OD1 B:ASP201 2.0 7.4 1.0 O B:HOH636 2.1 8.8 1.0 O B:HOH723 2.1 8.1 1.0 O B:HOH629 2.1 8.3 1.0 O B:HOH682 2.1 7.5 1.0 O B:HOH651 2.1 9.3 1.0 CG B:ASP201 3.1 7.9 1.0 OD2 B:ASP201 3.4 9.0 1.0 ZN B:ZN501 3.7 12.7 1.0 OE2 B:GLU230 4.0 10.7 1.0 O B:HOH749 4.1 24.4 1.0 O B:HOH679 4.1 10.0 1.0 CD2 B:HIS200 4.1 8.6 1.0 NE2 B:HIS233 4.2 8.1 1.0 O B:HIS200 4.2 7.3 1.0 OG1 B:THR271 4.2 10.2 1.0 O B:HOH720 4.2 13.0 1.0 CD2 B:HIS233 4.4 7.7 1.0 CB B:ASP201 4.4 8.0 1.0 OD2 B:ASP318 4.5 15.7 1.0 NE2 B:HIS200 4.6 7.8 1.0 CD2 B:HIS204 4.6 8.2 1.0 O B:THR271 4.7 11.7 1.0 O B:HOH672 4.7 22.9 1.0 CD2 B:HIS160 4.8 9.1 1.0 NE2 B:HIS160 4.8 10.9 1.0 CA B:ASP201 4.8 6.8 1.0 CB B:THR271 4.8 10.9 1.0 CG B:GLU230 4.8 8.8 1.0 NE2 B:HIS204 4.8 11.2 1.0 CD B:GLU230 4.8 11.6 1.0 C B:HIS200 4.9 8.1 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