Magnesium in PDB 4wcu: PDE4 Complexed with Inhibitor

All present enzymatic activity of PDE4 Complexed with Inhibitor:
3.1.4.53;

The structure of PDE4 Complexed with Inhibitor, PDB code: 4wcu was solved by M.D.Sorensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.85 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.232, 113.545, 160.535, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 30.4

The structure of PDE4 Complexed with Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium atom in the PDE4 Complexed with Inhibitor (pdb code 4wcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PDE4 Complexed with Inhibitor, PDB code: 4wcu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE4 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.6 occ:1.00 OD1 A:ASP201 2.4 24.2 1.0 O A:HOH693 2.5 19.9 1.0 CG A:ASP201 3.6 25.8 1.0 ZN A:ZN501 4.0 45.9 1.0 O A:HIS200 4.0 28.3 1.0 OD2 A:ASP201 4.0 26.2 1.0 OE2 A:GLU230 4.2 34.1 1.0 OG1 A:THR271 4.3 41.3 1.0 NE2 A:HIS233 4.3 29.4 1.0 CD2 A:HIS200 4.3 26.4 1.0 O A:HOH692 4.4 23.8 1.0 CD2 A:HIS233 4.4 27.8 1.0 C3 A:3KQ500 4.5 47.2 1.0 N4 A:3KQ500 4.5 47.0 1.0 O A:THR271 4.6 43.1 1.0 CD2 A:HIS204 4.6 30.9 1.0 OD2 A:ASP318 4.7 31.4 1.0 CG A:GLU230 4.7 33.3 1.0 CB A:THR271 4.7 41.9 1.0 NE2 A:HIS204 4.7 28.6 1.0 CB A:ASP201 4.8 26.0 1.0 NE2 A:HIS160 4.8 34.1 1.0 CD A:GLU230 4.8 33.9 1.0 CD2 A:HIS160 4.9 34.1 1.0 C A:HIS200 4.9 27.4 1.0 NE2 A:HIS200 4.9 27.4 1.0 CA A:ASP201 5.0 26.3 1.0 C2 A:3KQ500 5.0 46.5 1.0

Magnesium binding site 2 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE4 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:29.6 occ:1.00 OD1 B:ASP201 2.1 30.2 1.0 CG B:ASP201 3.2 30.6 1.0 OD2 B:ASP201 3.5 32.0 1.0 ZN B:ZN501 4.0 44.0 1.0 OE2 B:GLU230 4.2 31.3 1.0 NE2 B:HIS233 4.3 31.1 1.0 O B:HIS200 4.3 31.1 1.0 OG1 B:THR271 4.3 37.1 1.0 CD2 B:HIS233 4.3 28.9 1.0 CB B:ASP201 4.5 30.8 1.0 NE2 B:HIS160 4.6 35.1 1.0 CD2 B:HIS200 4.6 32.5 1.0 ND1 B:HIS204 4.6 34.2 1.0 C3 B:3KQ500 4.6 43.3 1.0 CD2 B:HIS160 4.6 34.9 1.0 N4 B:3KQ500 4.7 44.1 1.0 CE1 B:HIS204 4.8 33.1 1.0 OD2 B:ASP318 4.8 35.7 1.0 CB B:THR271 4.8 37.7 1.0 CA B:ASP201 4.8 30.9 1.0 O B:THR271 4.9 39.1 1.0 CD B:GLU230 4.9 29.1 1.0 CG B:GLU230 4.9 28.4 1.0

Magnesium binding site 3 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PDE4 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.9 occ:1.00 OD1 C:ASP201 2.2 30.8 1.0 CG C:ASP201 3.2 29.5 1.0 OD2 C:ASP201 3.5 31.2 1.0 ZN C:ZN501 3.9 48.1 1.0 NE2 C:HIS233 4.1 27.7 1.0 O C:HIS200 4.2 28.5 1.0 CD2 C:HIS233 4.3 26.7 1.0 O C:HOH629 4.3 22.1 1.0 OE2 C:GLU230 4.3 36.0 1.0 OG1 C:THR271 4.4 41.8 1.0 C3 C:3KQ500 4.5 45.3 1.0 CB C:ASP201 4.5 29.1 1.0 CD2 C:HIS200 4.6 28.7 1.0 CD2 C:HIS204 4.6 30.0 1.0 N4 C:3KQ500 4.6 45.4 1.0 OD2 C:ASP318 4.7 35.0 1.0 NE2 C:HIS204 4.7 28.4 1.0 CD2 C:HIS160 4.7 34.5 1.0 CB C:THR271 4.7 42.4 1.0 CG C:GLU230 4.8 32.4 1.0 NE2 C:HIS160 4.8 34.4 1.0 CA C:ASP201 4.8 28.9 1.0 CD C:GLU230 4.9 34.9 1.0 C2 C:3KQ500 4.9 45.3 1.0 NE2 C:HIS200 5.0 29.4 1.0

Magnesium binding site 4 out of 4 in the PDE4 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PDE4 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:30.9 occ:1.00 OD1 D:ASP201 2.5 37.0 1.0 CG D:ASP201 3.6 37.7 1.0 ZN D:ZN501 3.9 50.7 1.0 OD2 D:ASP201 4.0 38.4 1.0 OG1 D:THR271 4.0 42.4 1.0 OE2 D:GLU230 4.2 34.5 1.0 C3 D:3KQ500 4.3 52.6 1.0 CD2 D:HIS200 4.4 36.6 1.0 O D:HIS200 4.4 38.1 1.0 O D:HOH647 4.4 29.3 1.0 NE2 D:HIS233 4.5 32.1 1.0 OD2 D:ASP318 4.5 42.0 1.0 O D:THR271 4.5 43.4 1.0 N4 D:3KQ500 4.6 52.4 1.0 CB D:THR271 4.6 41.9 1.0 CD2 D:HIS233 4.6 33.2 1.0 C2 D:3KQ500 4.7 52.6 1.0 NE2 D:HIS160 4.8 39.1 1.0 CG D:GLU230 4.8 32.5 1.0 CD2 D:HIS204 4.8 33.6 1.0 CD2 D:HIS160 4.8 39.3 1.0 CD D:GLU230 4.9 34.1 1.0 NE2 D:HIS200 4.9 36.4 1.0 CB D:ASP201 5.0 37.1 1.0

J.Felding, M.D.Sorensen, T.D.Poulsen, J.Larsen, C.Andersson, P.Refer, K.Engell, L.G.Ladefoged, T.Thormann, A.M.Vinggaard, P.Hegardt, A.Sohoel, S.F.Nielsen. Discovery and Early Clinical Development of 2-{6-[2-(3,5-Dichloro-4-Pyridyl)Acetyl]-2, 3-Dimethoxyphenoxy}-N-Propylacetamide (Leo 29102), A Soft-Drug Inhibitor of Phosphodiesterase 4 For Topical Treatment of Atopic Dermatitis. J. Med. Chem. V. 57 5893 2014.
ISSN: ISSN 0022-2623
PubMed: 24984230
DOI: 10.1021/JM500378A