Iodine in PDB 4wzi: Crystal Structure of Crosslink Stabilized Long-Form PDE4B

All present enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B:
3.1.4.53;

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B, PDB code: 4wzi 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)	26.01 / 2.58
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.830, 137.830, 141.740, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.6

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B also contains other interesting chemical elements:

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

The binding sites of Iodine atom in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B (pdb code 4wzi). 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, PDB code: 4wzi:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I805 b:59.6 occ:1.00 O A:HOH980 3.4 37.3 1.0 NE A:ARG503 3.5 41.3 1.0 NH2 A:ARG503 3.5 27.4 1.0 O A:HOH1036 3.8 46.4 1.0 CE1 A:PHE484 3.8 24.7 1.0 CZ A:ARG503 3.9 55.7 1.0 CD1 A:PHE484 4.0 24.5 1.0 O A:ARG503 4.1 34.0 1.0 CB A:ARG503 4.2 27.7 1.0 CB A:ARG507 4.2 25.9 1.0 CD A:ARG507 4.4 22.9 1.0 CD1 A:LEU487 4.5 23.4 1.0 CD2 A:PHE495 4.5 27.5 1.0 CD A:ARG503 4.6 35.0 1.0 CG A:ARG503 4.7 35.7 1.0 C A:ARG503 4.7 34.8 1.0 CA A:ARG503 4.7 29.6 1.0 CG A:ARG507 4.8 31.4 1.0 O B:HOH1016 5.0 69.9 1.0 CZ A:PHE484 5.0 25.7 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:I804 b:53.9 occ:1.00 O B:HOH945 3.3 38.5 1.0 NE B:ARG503 3.5 43.3 1.0 NH2 B:ARG503 3.8 37.4 1.0 CE1 B:PHE484 3.8 27.6 1.0 O B:HOH967 4.0 47.5 1.0 CD1 B:PHE484 4.0 28.2 1.0 CZ B:ARG503 4.1 54.7 1.0 O B:ARG503 4.1 36.8 1.0 CB B:ARG503 4.2 30.2 1.0 CB B:ARG507 4.2 28.8 1.0 CD B:ARG507 4.3 23.4 1.0 CD1 B:LEU487 4.5 31.0 1.0 CD2 B:PHE495 4.5 33.7 1.0 CD B:ARG503 4.6 38.6 1.0 CG B:ARG503 4.6 39.7 1.0 C B:ARG503 4.7 37.8 1.0 CA B:ARG503 4.7 32.4 1.0 CG B:ARG507 4.7 25.0 1.0 O A:HOH1054 4.8 63.5 1.0 CZ B:PHE484 5.0 26.4 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.