Magnesium in PDB 4x0f: Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram

All present enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram:
3.1.4.53;

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram, PDB code: 4x0f was solved by P.Cedervall, J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	119.00 / 3.22
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.400, 137.400, 142.970, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 22.2

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram also contains other interesting chemical elements:

Iodine	(I)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram (pdb code 4x0f). 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 Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram, PDB code: 4x0f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram


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 Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:34.8 occ:1.00 OD1 A:ASP447 2.9 56.8 1.0 OG1 A:THR517 3.3 39.4 1.0 O A:HIS446 3.5 32.9 1.0 OE2 A:GLU476 3.6 62.7 1.0 O A:THR517 3.7 36.7 1.0 NE2 A:HIS479 3.8 41.7 1.0 CG A:ASP447 3.9 52.7 1.0 CD2 A:HIS479 3.9 41.9 1.0 CG A:GLU476 4.0 49.9 1.0 CB A:THR517 4.1 39.6 1.0 CD A:GLU476 4.2 70.9 1.0 CD2 A:HIS446 4.3 35.9 1.0 C A:THR517 4.3 36.1 1.0 OD2 A:ASP447 4.3 55.4 1.0 ZN A:ZN801 4.6 47.5 1.0 C A:HIS446 4.6 33.6 1.0 OD2 A:ASP564 4.6 62.6 1.0 CA A:THR517 4.9 31.0 1.0 CE1 A:HIS479 5.0 40.9 1.0 NE2 A:HIS446 5.0 35.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram


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 Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:39.7 occ:1.00 OD1 B:ASP447 2.7 60.9 1.0 OG1 B:THR517 3.1 65.6 1.0 O B:HIS446 3.2 39.8 1.0 CG B:ASP447 3.5 57.5 1.0 CD2 B:HIS446 3.6 43.8 1.0 O B:THR517 3.7 51.6 1.0 CB B:THR517 3.8 64.6 1.0 OD2 B:ASP447 3.9 63.2 1.0 NE2 B:HIS479 4.1 45.2 1.0 CD2 B:HIS479 4.1 44.6 1.0 OE2 B:GLU476 4.1 77.4 1.0 ZN B:ZN801 4.2 50.4 1.0 OD2 B:ASP564 4.2 62.7 1.0 C B:HIS446 4.2 39.8 1.0 CG B:GLU476 4.4 41.9 1.0 NE2 B:HIS446 4.4 44.3 1.0 C B:THR517 4.4 51.3 1.0 CG B:HIS446 4.5 41.5 1.0 CB B:ASP447 4.7 38.7 1.0 CD B:GLU476 4.7 66.8 1.0 CA B:THR517 4.7 48.1 1.0 CA B:ASP447 4.8 35.3 1.0 CG2 B:THR517 4.9 64.6 1.0 N B:ASP447 4.9 35.8 1.0 CB B:HIS446 5.0 37.4 1.0

P.Cedervall, A.Aulabaugh, K.F.Geoghegan, T.J.Mclellan, J.Pandit. Engineered Stabilization and Structural Analysis of the Autoinhibited Conformation of PDE4 Proc. Natl. Acad. Sci. 2015.