Magnesium in PDB 6imd: 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: 6imd 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)	39.02 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.400, 80.357, 163.441, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19

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 6imd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of PDE4D Complexed with A Novel Inhibitor, PDB code: 6imd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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:7.3 occ:1.00 OD1 A:ASP201 2.1 7.1 1.0 O A:HOH782 2.1 8.0 1.0 O A:HOH614 2.1 7.5 1.0 O A:HOH677 2.1 8.5 1.0 O A:HOH653 2.1 7.5 1.0 O A:HOH661 2.2 7.8 1.0 CG A:ASP201 3.0 6.2 1.0 OD2 A:ASP201 3.4 6.2 1.0 ZN A:ZN501 3.7 12.2 1.0 O A:HOH818 3.7 22.2 1.0 O A:HOH719 3.9 8.7 1.0 OE2 A:GLU230 4.0 11.1 1.0 NE2 A:HIS233 4.1 6.7 1.0 CD2 A:HIS200 4.1 6.0 1.0 O A:HOH746 4.2 14.2 1.0 O A:HIS200 4.2 6.9 1.0 OG1 A:THR271 4.2 8.4 1.0 CD2 A:HIS233 4.3 7.0 1.0 CB A:ASP201 4.4 6.8 1.0 OD2 A:ASP318 4.4 15.1 1.0 CD2 A:HIS204 4.5 8.1 1.0 NE2 A:HIS200 4.5 5.7 1.0 O A:HOH709 4.6 24.6 1.0 CB A:THR271 4.7 9.8 1.0 O A:THR271 4.7 11.2 1.0 NE2 A:HIS160 4.7 10.2 1.0 CD2 A:HIS160 4.7 9.2 1.0 CG A:GLU230 4.8 8.9 1.0 NE2 A:HIS204 4.8 7.6 1.0 CA A:ASP201 4.8 6.4 1.0 CD A:GLU230 4.8 8.6 1.0 C A:HIS200 5.0 6.1 1.0

Magnesium binding site 2 out of 4 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:15.6 occ:1.00 O A:ASP151 2.0 11.8 1.0 O A:HOH741 2.1 15.7 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 8.9 1.0 CA A:ASP151 3.9 10.8 1.0 CA A:HIS154 4.0 10.2 1.0 N A:TYR153 4.0 8.7 1.0 N A:ALA155 4.1 17.2 1.0 N A:HIS152 4.1 10.8 1.0 N A:HIS154 4.1 9.6 1.0 C A:HIS152 4.1 11.1 1.0 CA A:HIS152 4.2 10.6 1.0 O A:HOH683 4.2 14.6 1.0 CA A:TYR153 4.3 8.6 1.0 O A:GLU150 4.4 10.0 1.0 C A:HIS154 4.5 14.2 1.0 O A:HOH743 4.5 17.5 1.0 O A:HIS152 4.7 9.9 1.0 CB A:ASP151 4.8 12.3 1.0

Magnesium binding site 3 out of 4 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 A:Mg504 b:23.7 occ:1.00 O A:HOH657 2.0 26.9 1.0 O A:HOH635 2.0 23.5 1.0 O A:HOH824 2.1 30.7 1.0 O A:HOH855 2.1 32.6 1.0 O A:HOH610 4.0 31.4 1.0 OD2 A:ASP98 4.2 25.3 1.0 OE2 A:GLU95 4.2 26.2 1.0 O A:HOH606 4.3 29.6 1.0 CE1 A:HIS105 4.3 20.3 1.0 OE1 A:GLU95 4.4 21.6 1.0 CD A:GLU95 4.6 22.0 1.0 ND1 A:HIS105 4.7 17.8 1.0 CE A:LYS94 4.9 43.0 1.0

Magnesium binding site 4 out of 4 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 4 of Crystal Structure of PDE4D Complexed with A Novel Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:8.9 occ:1.00 OD1 B:ASP201 2.0 8.2 1.0 O B:HOH616 2.0 9.2 1.0 O B:HOH737 2.0 11.0 1.0 O B:HOH636 2.1 8.8 1.0 O B:HOH650 2.1 9.2 1.0 O B:HOH669 2.1 9.3 1.0 CG B:ASP201 3.1 10.0 1.0 OD2 B:ASP201 3.4 8.6 1.0 ZN B:ZN502 3.7 15.2 1.0 O B:HOH757 3.8 30.6 1.0 O B:HOH696 3.9 12.1 1.0 OE2 B:GLU230 4.0 11.4 1.0 CD2 B:HIS200 4.1 8.8 1.0 NE2 B:HIS233 4.1 9.5 1.0 O B:HIS200 4.2 8.9 1.0 O B:HOH730 4.2 13.1 1.0 OG1 B:THR271 4.2 10.1 1.0 CD2 B:HIS233 4.3 9.2 1.0 OD2 B:ASP318 4.4 21.1 1.0 CB B:ASP201 4.4 7.6 1.0 NE2 B:HIS200 4.5 9.5 1.0 O B:HOH649 4.5 20.7 1.0 CD2 B:HIS204 4.6 9.4 1.0 O B:THR271 4.7 12.9 1.0 CB B:THR271 4.8 12.2 1.0 CD2 B:HIS160 4.8 9.6 1.0 CA B:ASP201 4.8 6.6 1.0 NE2 B:HIS160 4.8 12.6 1.0 CG B:GLU230 4.8 9.0 1.0 NE2 B:HIS204 4.8 10.2 1.0 CD B:GLU230 4.9 10.3 1.0 C B:HIS200 5.0 8.7 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