Magnesium in PDB 6im6: 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: 6im6 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)	40.17 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.081, 80.346, 163.350, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24

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 6im6). 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: 6im6:
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:4.7 occ:1.00 O A:HOH632 1.9 4.0 1.0 O A:HOH673 2.1 4.8 1.0 OD1 A:ASP201 2.1 2.8 1.0 O A:HOH762 2.1 3.8 1.0 O A:HOH664 2.1 6.1 1.0 O A:HOH694 2.2 3.4 1.0 CG A:ASP201 3.1 2.7 1.0 OD2 A:ASP201 3.4 2.5 1.0 O A:HOH779 3.7 14.6 1.0 ZN A:ZN501 3.7 10.9 1.0 O A:HOH752 4.0 7.8 1.0 OE2 A:GLU230 4.1 7.6 1.0 NE2 A:HIS233 4.1 6.0 1.0 CD2 A:HIS200 4.2 3.6 1.0 O A:HIS200 4.2 2.8 1.0 OG1 A:THR271 4.3 6.5 1.0 CD2 A:HIS233 4.3 3.7 1.0 O A:HOH747 4.4 12.1 1.0 OD2 A:ASP318 4.4 9.7 1.0 CD2 A:HIS204 4.4 5.1 1.0 CB A:ASP201 4.5 3.8 1.0 NE2 A:HIS200 4.6 3.3 1.0 O A:THR271 4.7 8.8 1.0 CB A:THR271 4.7 7.4 1.0 NE2 A:HIS204 4.7 6.3 1.0 CA A:ASP201 4.8 3.1 1.0 CD2 A:HIS160 4.8 6.3 1.0 CG A:GLU230 4.8 8.0 1.0 CD A:GLU230 4.9 6.4 1.0 NE2 A:HIS160 5.0 6.7 1.0 C A:HIS200 5.0 4.0 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:25.0 occ:1.00 O A:HOH726 2.1 23.4 1.0 O A:HOH646 2.1 24.2 1.0 OD1 A:ASP203 2.1 11.9 1.0 NE2 A:HIS154 2.2 15.1 1.0 O A:HOH682 2.2 16.7 1.0 CE1 A:HIS154 2.9 21.8 1.0 CG A:ASP203 3.0 12.7 1.0 OD2 A:ASP203 3.3 8.9 1.0 CD2 A:HIS154 3.4 14.9 1.0 O A:HOH716 3.9 19.5 1.0 O A:ASP203 4.1 5.3 1.0 ND1 A:HIS154 4.1 20.9 1.0 CB A:ASP203 4.3 5.0 1.0 CG A:HIS154 4.4 12.0 1.0 CA A:ASP203 4.5 5.7 1.0 C A:ASP203 4.6 4.9 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:12.7 occ:1.00 O A:HOH724 2.1 13.4 1.0 O A:ASP151 2.2 7.9 1.0 O A:TYR153 2.2 8.8 1.0 C A:ASP151 3.2 7.7 1.0 C A:TYR153 3.3 9.6 1.0 OD1 A:ASP151 3.9 24.5 1.0 CA A:HIS154 3.9 8.8 1.0 N A:ALA155 4.0 11.9 1.0 CA A:ASP151 4.0 7.9 1.0 N A:HIS154 4.0 8.3 1.0 N A:TYR153 4.1 5.0 1.0 N A:HIS152 4.2 6.1 1.0 O A:HOH665 4.2 13.7 1.0 C A:HIS152 4.3 5.8 1.0 CA A:HIS152 4.3 6.4 1.0 CA A:TYR153 4.4 5.2 1.0 C A:HIS154 4.4 13.0 1.0 CG A:ASP151 4.4 24.3 1.0 O A:GLU150 4.4 6.9 1.0 O A:HOH716 4.6 19.5 1.0 O A:HIS152 4.8 6.5 1.0 CB A:ASP151 4.9 11.3 1.0 CB A:ALA155 5.0 16.0 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:Mg502 b:7.3 occ:1.00 O B:HOH696 2.0 7.0 1.0 OD1 B:ASP201 2.1 7.7 1.0 O B:HOH604 2.1 8.1 1.0 O B:HOH661 2.1 5.4 1.0 O B:HOH621 2.1 4.7 1.0 O B:HOH637 2.2 7.5 1.0 CG B:ASP201 3.1 6.3 1.0 OD2 B:ASP201 3.4 5.2 1.0 O B:HOH709 3.7 18.6 1.0 ZN B:ZN501 3.8 13.0 1.0 OE1 B:GLU230 4.0 8.4 1.0 O B:HOH678 4.1 10.8 1.0 O B:HIS200 4.1 4.4 1.0 CD2 B:HIS200 4.1 6.0 1.0 NE2 B:HIS233 4.2 5.9 1.0 OG1 B:THR271 4.2 8.0 1.0 O B:HOH688 4.3 12.0 1.0 CD2 B:HIS233 4.4 5.2 1.0 OD2 B:ASP318 4.4 13.9 1.0 CB B:ASP201 4.5 5.0 1.0 CD2 B:HIS204 4.5 7.2 1.0 NE2 B:HIS200 4.6 6.0 1.0 O B:THR271 4.7 11.3 1.0 NE2 B:HIS204 4.8 7.5 1.0 CB B:THR271 4.8 9.8 1.0 CD2 B:HIS160 4.8 6.0 1.0 CG B:GLU230 4.8 6.7 1.0 CA B:ASP201 4.8 5.5 1.0 CD B:GLU230 4.8 10.1 1.0 NE2 B:HIS160 4.9 8.5 1.0 C B:HIS200 5.0 5.9 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