Magnesium in PDB 6lrm: Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin:
3.1.4.53;

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin, PDB code: 6lrm was solved by X.L.Zhang, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.42 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.879, 80.448, 163.733, 90, 90, 90
R / Rfree (%)	18.1 / 20.2

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin (pdb code 6lrm). 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 Catalytic Domain in Complex with Arctigenin, PDB code: 6lrm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin


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 Catalytic Domain in Complex with Arctigenin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:6.8 occ:1.00 O A:HOH632 2.0 7.8 1.0 OD1 A:ASP201 2.1 6.9 1.0 O A:HOH769 2.1 9.1 1.0 O A:HOH679 2.1 8.4 1.0 O A:HOH631 2.1 8.9 1.0 O A:HOH670 2.1 8.6 1.0 CG A:ASP201 3.1 6.8 1.0 OD2 A:ASP201 3.4 6.8 1.0 ZN A:ZN501 3.7 11.3 1.0 O A:HOH742 4.0 9.1 1.0 OE2 A:GLU230 4.0 10.2 1.0 NE2 A:HIS233 4.1 8.0 1.0 CD2 A:HIS200 4.2 6.7 1.0 O A:HIS200 4.2 7.3 1.0 OG1 A:THR271 4.3 8.3 1.0 CD2 A:HIS233 4.4 8.3 1.0 O A:HOH644 4.4 13.2 1.0 CB A:ASP201 4.4 6.8 1.0 OD2 A:ASP318 4.5 11.6 1.0 NE2 A:HIS200 4.5 6.8 1.0 CD2 A:HIS204 4.5 7.8 1.0 O A:THR271 4.6 10.1 1.0 CE A:MET273 4.7 17.8 1.0 CA A:ASP201 4.8 6.8 1.0 CG A:GLU230 4.8 9.8 1.0 CE1 A:HIS160 4.8 9.7 1.0 NE2 A:HIS204 4.8 8.5 1.0 CD A:GLU230 4.9 10.4 1.0 ND1 A:HIS160 4.9 7.9 1.0 CB A:THR271 4.9 8.8 1.0 C A:HIS200 5.0 6.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin


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 Catalytic Domain in Complex with Arctigenin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:10.3 occ:1.00 OD1 B:ASP201 2.1 10.7 1.0 O B:HOH617 2.1 11.2 1.0 O B:HOH716 2.1 11.0 1.0 O B:HOH657 2.1 10.1 1.0 O B:HOH624 2.1 10.8 1.0 O B:HOH663 2.2 11.1 1.0 CG B:ASP201 3.1 11.1 1.0 OD2 B:ASP201 3.4 11.4 1.0 ZN B:ZN502 3.7 14.6 1.0 OE2 B:GLU230 4.0 11.3 1.0 O B:HOH681 4.1 11.5 1.0 CD2 B:HIS200 4.1 11.8 1.0 NE2 B:HIS233 4.1 9.7 1.0 O B:HIS200 4.2 10.8 1.0 OG1 B:THR271 4.4 11.1 1.0 O B:HOH640 4.4 14.2 1.0 CD2 B:HIS233 4.4 9.8 1.0 CB B:ASP201 4.4 11.4 1.0 OD1 B:ASP318 4.5 11.8 1.0 NE2 B:HIS200 4.5 12.1 1.0 ND1 B:HIS204 4.6 11.6 1.0 O B:THR271 4.6 12.2 1.0 CE B:MET273 4.7 20.1 1.0 NE2 B:HIS160 4.8 13.2 1.0 CG B:GLU230 4.8 10.0 1.0 CA B:ASP201 4.8 11.2 1.0 CD2 B:HIS160 4.8 11.2 1.0 CD B:GLU230 4.9 11.5 1.0 CE1 B:HIS204 4.9 10.0 1.0 CB B:THR271 4.9 12.1 1.0 C B:HIS200 5.0 11.3 1.0

H.Li, X.L.Zhang, M.T.Liu, C.L.Feng, C.Fan, H.X.Su, Y.Zhou, Q.Qi, Y.C.Xu, W.Tang. Identification of PDE4 As the Therapeutic Target of Arctigenin in Alleviating Psoriatic Skin Inflammation To Be Published.