Magnesium in PDB 6f6u: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B:
3.1.4.53;

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B, PDB code: 6f6u was solved by T.Prosdocimi, S.Donini, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.71 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.827, 98.936, 119.532, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B (pdb code 6f6u). 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 the PDE4D Catalytic Domain in Complex with Gebr- 7B, PDB code: 6f6u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B


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 the PDE4D Catalytic Domain in Complex with Gebr- 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:13.2 occ:1.00 O A:HOH783 2.1 13.7 1.0 OD1 A:ASP367 2.1 13.4 1.0 O A:HOH893 2.1 12.4 1.0 O A:HOH821 2.1 17.5 1.0 O A:HOH799 2.2 15.6 1.0 O A:HOH875 2.2 16.3 1.0 CG A:ASP367 3.1 17.2 1.0 OD2 A:ASP367 3.4 12.5 1.0 ZN A:ZN602 3.7 19.0 1.0 O A:HOH877 4.0 19.8 1.0 CD2 A:HIS366 4.1 15.1 1.0 OE2 A:GLU396 4.1 18.4 1.0 O A:HOH899 4.1 17.5 1.0 O A:HIS366 4.2 16.6 1.0 NE2 A:HIS399 4.2 14.9 1.0 O A:HOH717 4.3 35.0 1.0 OG1 A:THR437 4.3 15.5 1.0 O A:HOH934 4.4 35.1 1.0 CD2 A:HIS399 4.4 12.2 1.0 CB A:ASP367 4.4 13.2 1.0 NE2 A:HIS366 4.5 11.1 1.0 OD2 A:ASP484 4.5 24.6 1.0 CD2 A:HIS370 4.5 13.1 1.0 O A:THR437 4.8 20.2 1.0 CA A:ASP367 4.8 12.5 1.0 CD2 A:HIS326 4.8 18.2 1.0 NE2 A:HIS370 4.8 18.6 1.0 NE2 A:HIS326 4.8 17.2 1.0 CB A:THR437 4.8 14.9 1.0 CG A:GLU396 4.9 14.8 1.0 CD A:GLU396 4.9 20.0 1.0 C A:HIS366 5.0 14.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B


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 the PDE4D Catalytic Domain in Complex with Gebr- 7B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:41.5 occ:1.00 O A:HOH710 2.7 41.5 1.0 OD2 A:ASP264 3.6 45.1 1.0 OD1 A:ASP264 3.8 35.5 1.0 CG A:ASP264 4.1 39.0 1.0 O A:LYS260 4.6 32.8 1.0 NZ A:LYS260 4.8 51.2 1.0 OE1 A:GLU263 4.9 42.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 7B


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 the PDE4D Catalytic Domain in Complex with Gebr- 7B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:13.1 occ:1.00 O B:HOH780 2.0 13.7 1.0 O B:HOH835 2.0 20.6 1.0 O B:HOH857 2.0 15.6 1.0 OD1 B:ASP367 2.1 13.3 1.0 O B:HOH767 2.2 13.0 1.0 O B:HOH838 2.2 19.2 1.0 CG B:ASP367 3.1 15.1 1.0 OD2 B:ASP367 3.4 14.6 1.0 ZN B:ZN602 3.6 19.9 1.0 O B:HOH704 3.9 22.1 0.8 O B:HOH851 4.0 19.9 1.0 OE2 B:GLU396 4.1 17.5 1.0 O B:HOH865 4.1 20.2 1.0 CD2 B:HIS366 4.1 14.8 1.0 NE2 B:HIS399 4.1 14.0 1.0 O B:HIS366 4.2 13.9 1.0 O B:HOH874 4.3 31.7 1.0 OG1 B:THR437 4.3 15.8 1.0 CD2 B:HIS399 4.4 15.2 1.0 O B:HOH710 4.4 35.7 1.0 CB B:ASP367 4.4 14.7 1.0 NE2 B:HIS366 4.5 13.5 1.0 OD2 B:ASP484 4.5 24.5 1.0 CD2 B:HIS326 4.6 12.9 1.0 O B:HOH922 4.6 37.6 1.0 CD2 B:HIS370 4.6 14.8 1.0 NE2 B:HIS326 4.6 17.2 1.0 O B:THR437 4.8 17.5 1.0 CB B:THR437 4.8 14.8 1.0 CA B:ASP367 4.8 12.2 1.0 CG B:GLU396 4.9 14.9 1.0 CD B:GLU396 4.9 15.6 1.0 NE2 B:HIS370 4.9 16.8 1.0 C B:HIS366 5.0 16.6 1.0

T.Prosdocimi, L.Mollica, S.Donini, M.S.Semrau, A.P.Lucarelli, E.Aiolfi, A.Cavalli, P.Storici, S.Alfei, C.Brullo, O.Bruno, E.Parisini. Molecular Bases of PDE4D Inhibition By Memory-Enhancing Gebr Library Compounds. Biochemistry V. 57 2876 2018.
ISSN: ISSN 1520-4995
PubMed: 29652483
DOI: 10.1021/ACS.BIOCHEM.8B00288