Magnesium in PDB 6imi: 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: 6imi was solved by X.Zhang, H.Su, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.414, 80.530, 163.844, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.7

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 6imi). 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: 6imi:
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:Mg501 b:7.8 occ:1.00 OD1 A:ASP201 2.0 6.8 1.0 O A:HOH786 2.1 8.5 1.0 O A:HOH703 2.1 8.3 1.0 O A:HOH657 2.1 7.6 1.0 O A:HOH667 2.1 7.9 1.0 O A:HOH618 2.1 8.1 1.0 CG A:ASP201 3.1 7.2 1.0 OD2 A:ASP201 3.4 6.4 1.0 ZN A:ZN503 3.8 13.7 1.0 O A:HOH816 3.8 33.8 1.0 OE2 A:GLU230 4.0 11.2 1.0 O A:HOH702 4.1 7.9 1.0 NE2 A:HIS233 4.1 7.0 1.0 CD2 A:HIS200 4.2 6.0 1.0 O A:HIS200 4.2 7.7 1.0 O A:HOH745 4.2 13.1 1.0 OG1 A:THR271 4.3 8.4 1.0 CD2 A:HIS233 4.4 7.0 1.0 CB A:ASP201 4.4 6.6 1.0 OD2 A:ASP318 4.5 13.1 1.0 CD2 A:HIS204 4.5 7.5 1.0 NE2 A:HIS200 4.5 6.7 1.0 O A:THR271 4.7 10.9 1.0 CG A:GLU230 4.8 11.9 1.0 CB A:THR271 4.8 11.1 1.0 NE2 A:HIS160 4.8 10.1 1.0 CA A:ASP201 4.8 6.7 1.0 CD2 A:HIS160 4.8 8.9 1.0 NE2 A:HIS204 4.8 9.9 1.0 CD A:GLU230 4.9 14.2 1.0 C A:HIS200 5.0 6.6 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:Mg502 b:17.7 occ:1.00 O A:ASP151 2.0 12.0 1.0 O A:TYR153 2.1 12.2 1.0 C A:ASP151 3.1 10.8 1.0 C A:TYR153 3.3 11.2 1.0 CA A:ASP151 4.0 11.0 1.0 CA A:HIS154 4.0 10.5 1.0 N A:TYR153 4.0 8.9 1.0 N A:HIS152 4.1 10.7 1.0 N A:HIS154 4.1 9.6 1.0 N A:ALA155 4.1 20.4 1.0 C A:HIS152 4.2 14.6 1.0 CA A:HIS152 4.2 10.4 1.0 O A:HOH701 4.2 16.6 1.0 CA A:TYR153 4.3 8.5 1.0 O A:GLU150 4.4 11.1 1.0 C A:HIS154 4.5 14.0 1.0 O A:HOH732 4.6 18.9 1.0 O A:HIS152 4.8 11.0 1.0 CB A:ASP151 4.8 16.9 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:Mg501 b:9.1 occ:1.00 OD1 B:ASP201 2.0 8.3 1.0 O B:HOH615 2.1 9.1 1.0 O B:HOH702 2.1 10.0 1.0 O B:HOH625 2.1 8.9 1.0 O B:HOH661 2.1 8.6 1.0 O B:HOH635 2.1 9.2 1.0 CG B:ASP201 3.0 9.2 1.0 OD2 B:ASP201 3.4 9.1 1.0 ZN B:ZN502 3.8 18.0 1.0 O B:HOH731 3.8 32.5 1.0 OE2 B:GLU230 4.0 13.7 1.0 O B:HOH674 4.1 10.5 1.0 CD2 B:HIS200 4.1 9.4 1.0 O B:HIS200 4.1 8.8 1.0 NE2 B:HIS233 4.2 9.6 1.0 O B:HOH697 4.3 14.6 1.0 OG1 B:THR271 4.3 10.9 1.0 CB B:ASP201 4.4 7.9 1.0 CD2 B:HIS233 4.4 8.9 1.0 OD2 B:ASP318 4.5 22.2 1.0 NE2 B:HIS200 4.5 10.0 1.0 CD2 B:HIS204 4.6 10.0 1.0 O B:THR271 4.7 13.4 1.0 CD2 B:HIS160 4.8 11.8 1.0 CA B:ASP201 4.8 8.7 1.0 NE2 B:HIS160 4.8 12.3 1.0 NE2 B:HIS204 4.8 10.4 1.0 CB B:THR271 4.8 14.2 1.0 CG B:GLU230 4.9 9.9 1.0 O B:HOH715 4.9 52.5 1.0 CD B:GLU230 4.9 15.6 1.0 C B:HIS200 5.0 10.1 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