Magnesium in PDB 6imr: 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: 6imr 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)	30.90 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.120, 80.624, 163.669, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.7

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 6imr). 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: 6imr:
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:5.5 occ:1.00 O A:HOH656 2.0 5.8 1.0 O A:HOH803 2.1 7.3 1.0 OD1 A:ASP201 2.1 4.8 1.0 O A:HOH697 2.1 7.3 1.0 O A:HOH648 2.1 6.9 1.0 O A:HOH612 2.1 5.8 1.0 CG A:ASP201 3.1 3.3 1.0 OD2 A:ASP201 3.4 4.0 1.0 O A:HOH811 3.6 13.7 1.0 ZN A:ZN501 3.8 12.0 1.0 O A:HOH788 4.0 7.1 1.0 NE2 A:HIS233 4.1 6.0 1.0 OE2 A:GLU230 4.1 10.1 1.0 CD2 A:HIS200 4.1 5.1 1.0 O A:HIS200 4.2 5.3 1.0 O A:HOH607 4.3 19.5 1.0 OG1 A:THR271 4.3 7.2 1.0 O A:HOH737 4.3 14.1 1.0 CD2 A:HIS233 4.3 6.1 1.0 CB A:ASP201 4.4 4.5 1.0 CD2 A:HIS204 4.5 6.3 1.0 OD2 A:ASP318 4.5 9.3 1.0 NE2 A:HIS200 4.5 4.5 1.0 O A:THR271 4.7 8.1 1.0 O A:HOH690 4.7 19.3 1.0 CB A:THR271 4.7 8.3 1.0 NE2 A:HIS204 4.8 7.5 1.0 CA A:ASP201 4.8 4.4 1.0 CD2 A:HIS160 4.8 6.7 1.0 CG A:GLU230 4.8 8.2 1.0 CD A:GLU230 4.9 8.4 1.0 NE2 A:HIS160 4.9 9.2 1.0 C A:HIS200 5.0 5.4 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:6.9 occ:1.00 O B:HOH728 2.0 9.4 1.0 OD1 B:ASP201 2.0 6.2 1.0 O B:HOH642 2.1 7.6 1.0 O B:HOH670 2.1 7.8 1.0 O B:HOH636 2.1 8.2 1.0 O B:HOH633 2.2 8.4 1.0 CG B:ASP201 3.1 6.8 1.0 OD2 B:ASP201 3.4 7.4 1.0 O B:HOH737 3.7 20.0 1.0 ZN B:ZN501 3.8 15.0 1.0 O B:HOH714 4.0 10.2 1.0 OE2 B:GLU230 4.0 11.5 1.0 CD2 B:HIS200 4.1 8.1 1.0 NE2 B:HIS233 4.1 6.7 1.0 O B:HIS200 4.1 7.3 1.0 O B:HOH709 4.2 13.8 1.0 OG1 B:THR271 4.2 9.3 1.0 O B:HOH605 4.3 22.1 1.0 CD2 B:HIS233 4.4 7.1 1.0 CB B:ASP201 4.4 6.2 1.0 CD2 B:HIS204 4.5 8.0 1.0 NE2 B:HIS200 4.5 7.5 1.0 OD2 B:ASP318 4.5 13.9 1.0 O B:THR271 4.7 12.6 1.0 CD2 B:HIS160 4.7 7.7 1.0 NE2 B:HIS204 4.8 9.9 1.0 CA B:ASP201 4.8 6.6 1.0 CB B:THR271 4.8 10.4 1.0 O B:HOH641 4.8 19.9 1.0 NE2 B:HIS160 4.9 10.5 1.0 CG B:GLU230 4.9 8.2 1.0 CD B:GLU230 4.9 10.1 1.0 C B:HIS200 5.0 6.5 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