Magnesium in PDB 5wh6: Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91):
3.1.4.53;

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6 was solved by H.Ke, H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.948, 80.197, 163.670, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.4

The structure of Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91) also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91) (pdb code 5wh6). 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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91), PDB code: 5wh6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:16.4 occ:1.00 O A:HOH702 2.1 16.2 1.0 O A:HOH726 2.1 14.2 1.0 O A:HOH722 2.1 18.0 1.0 O A:HOH850 2.1 15.1 1.0 O A:HOH787 2.1 15.1 1.0 OD1 A:ASP201 2.2 15.4 1.0 CG A:ASP201 3.2 15.7 1.0 OD2 A:ASP201 3.5 15.7 1.0 ZN A:ZN602 3.9 17.9 1.0 OE2 A:GLU230 4.0 19.3 1.0 O A:HOH806 4.1 15.1 1.0 NE2 A:HIS233 4.2 15.3 1.0 O A:HIS200 4.2 14.6 1.0 CD2 A:HIS200 4.2 15.2 1.0 OG1 A:THR271 4.3 18.2 1.0 O A:HOH797 4.3 23.0 1.0 OD2 A:ASP318 4.4 17.9 1.0 CD2 A:HIS233 4.4 15.3 1.0 CD2 A:HIS204 4.5 17.0 1.0 CB A:ASP201 4.5 15.3 1.0 O A:THR271 4.6 18.8 1.0 NE2 A:HIS200 4.7 15.2 1.0 NE2 A:HIS160 4.7 18.7 1.0 CB A:THR271 4.7 18.4 1.0 NE2 A:HIS204 4.7 17.2 1.0 CG A:GLU230 4.8 18.6 1.0 CD2 A:HIS160 4.8 18.5 1.0 CD A:GLU230 4.8 18.7 1.0 CA A:ASP201 4.8 15.4 1.0 C16 A:AKJ601 4.9 26.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:21.9 occ:1.00 O A:HOH836 2.1 25.4 1.0 O A:ASP151 2.2 21.2 1.0 O A:TYR153 2.2 20.1 1.0 C A:ASP151 3.2 20.8 1.0 C A:TYR153 3.3 19.5 1.0 CA A:HIS154 3.9 22.2 1.0 N A:ALA155 4.0 25.2 1.0 N A:HIS154 4.0 20.6 1.0 CA A:ASP151 4.1 22.1 1.0 N A:TYR153 4.1 18.0 1.0 N A:HIS152 4.2 19.6 1.0 O A:HOH774 4.2 23.3 1.0 C A:HIS152 4.3 18.5 1.0 CA A:HIS152 4.3 18.9 1.0 CA A:TYR153 4.4 18.1 1.0 C A:HIS154 4.5 23.4 1.0 O A:GLU150 4.5 19.7 1.0 O A:HOH903 4.6 48.4 1.0 O A:HOH843 4.6 28.2 1.0 O A:HIS152 4.9 18.2 1.0 CB A:ALA155 4.9 26.9 1.0 CB A:ASP151 4.9 23.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of PDE4D2 in Complex with Inhibitor (S_ZL-N-91)


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 PDE4D2 in Complex with Inhibitor (S_ZL-N-91) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:15.8 occ:1.00 O B:HOH757 2.0 16.9 1.0 O B:HOH820 2.1 15.5 1.0 O B:HOH702 2.1 19.4 1.0 O B:HOH716 2.1 17.1 1.0 O B:HOH782 2.2 16.6 1.0 OD1 B:ASP201 2.2 15.8 1.0 CG B:ASP201 3.2 16.0 1.0 OD2 B:ASP201 3.5 17.6 1.0 ZN B:ZN602 4.0 20.1 1.0 OE2 B:GLU230 4.0 18.8 1.0 O B:HOH813 4.2 21.9 1.0 O B:HOH740 4.2 17.7 1.0 O B:HIS200 4.2 16.9 1.0 CD2 B:HIS200 4.2 17.5 1.0 NE2 B:HIS233 4.2 17.1 1.0 OG1 B:THR271 4.2 18.8 1.0 CD2 B:HIS233 4.4 16.9 1.0 OD2 B:ASP318 4.4 20.4 1.0 O B:HOH703 4.5 41.3 1.0 CB B:ASP201 4.5 16.2 1.0 CD2 B:HIS204 4.6 18.7 1.0 NE2 B:HIS200 4.6 17.9 1.0 O B:THR271 4.6 19.8 1.0 NE2 B:HIS160 4.7 17.4 1.0 CB B:THR271 4.8 19.2 1.0 NE2 B:HIS204 4.8 19.3 1.0 CD2 B:HIS160 4.8 17.5 1.0 CG B:GLU230 4.8 17.6 1.0 CD B:GLU230 4.8 18.1 1.0 CA B:ASP201 4.9 16.3 1.0 C15 B:AKJ601 4.9 33.7 1.0

X.Feng, H.Wang, M.Ye, X.T.Xu, Y.Xu, W.Yang, H.T.Zhang, G.Song, H.Ke. Identification of A PDE4-Specific Pocket For the Design of Selective Inhibitors. Biochemistry V. 57 4518 2018.
ISSN: ISSN 0006-2960
PubMed: 29975048
DOI: 10.1021/ACS.BIOCHEM.8B00336