Iodine 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:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	3 atoms

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

Iodine 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 Iodine with other atoms in the I 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:I803 b:91.1 occ:1.00 NE A:ARG503 3.8 64.7 1.0 NH2 A:ARG503 3.9 25.1 1.0 CE1 A:PHE484 4.1 42.5 1.0 CD1 A:PHE484 4.2 41.1 1.0 CZ A:ARG503 4.2 65.0 1.0 CB A:ARG503 4.3 30.5 1.0 CB A:ARG507 4.4 24.1 1.0 CD2 A:PHE495 4.4 38.4 1.0 O A:ARG503 4.5 38.5 1.0 CD1 A:LEU487 4.6 31.7 1.0 CD A:ARG507 4.7 17.1 1.0 CG A:ARG507 4.8 22.5 1.0 CD A:ARG503 4.8 56.9 1.0 CB A:PHE495 4.8 36.9 1.0 CA A:ARG503 4.8 33.9 1.0 C A:ARG503 4.9 38.6 1.0 CG A:ARG503 4.9 40.6 1.0

Iodine 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 Iodine with other atoms in the I 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:I802 b:80.5 occ:1.00 NE B:ARG503 3.9 58.7 1.0 CE1 B:PHE484 4.0 44.1 1.0 NH2 B:ARG503 4.0 44.4 1.0 CD1 B:PHE484 4.1 43.4 1.0 CB B:ARG507 4.2 26.5 1.0 CB B:ARG503 4.3 47.7 1.0 O B:ARG503 4.4 49.6 1.0 CZ B:ARG503 4.4 72.3 1.0 CD2 B:PHE495 4.4 55.7 1.0 CD B:ARG507 4.6 17.9 1.0 CD1 B:LEU487 4.6 41.2 1.0 CG B:ARG507 4.7 21.1 1.0 C B:ARG503 4.8 50.1 1.0 CA B:ARG503 4.8 47.5 1.0 CD B:ARG503 4.9 53.5 1.0 CG B:ARG503 4.9 53.8 1.0 CB B:PHE495 4.9 54.1 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.