Zinc 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
Iodine	(I)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B, PDB code: 4wzi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn801 b:30.6 occ:1.00 O A:HOH1089 1.9 40.4 1.0 NE2 A:HIS410 2.0 22.6 1.0 NE2 A:HIS446 2.1 27.2 1.0 OD2 A:ASP447 2.2 37.4 1.0 OD1 A:ASP564 2.2 32.5 1.0 CD2 A:HIS446 3.0 26.3 1.0 CE1 A:HIS410 3.0 22.2 1.0 CD2 A:HIS410 3.0 23.1 1.0 CG A:ASP564 3.1 32.9 1.0 CE1 A:HIS446 3.1 26.8 1.0 CG A:ASP447 3.2 29.6 1.0 OD2 A:ASP564 3.3 34.8 1.0 O A:HOH996 3.7 43.4 1.0 OD1 A:ASP447 3.8 28.9 1.0 MG A:MG804 3.8 53.6 1.0 CG A:HIS446 4.1 25.2 1.0 CD2 A:HIS406 4.1 28.5 1.0 ND1 A:HIS410 4.2 22.6 1.0 CG A:HIS410 4.2 22.2 1.0 ND1 A:HIS446 4.2 27.1 1.0 CB A:ASP447 4.4 20.5 1.0 CB A:ASP564 4.4 25.9 1.0 O A:HOH948 4.4 23.8 1.0 NE2 A:HIS406 4.5 28.0 1.0 CG2 A:VAL414 4.5 24.8 1.0 O A:HOH950 4.9 23.1 1.0 CA A:ASP564 5.0 25.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Crosslink Stabilized Long-Form PDE4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:38.0 occ:1.00 O A:HOH906 1.9 39.2 1.0 ND1 A:HIS491 1.9 30.9 1.0 CE1 A:HIS491 2.7 31.6 1.0 CG A:HIS491 3.1 29.9 1.0 CB A:HIS491 3.6 27.4 1.0 NE2 A:HIS491 3.9 31.7 1.0 O A:HOH907 4.0 34.2 1.0 OD2 A:ASP386 4.0 51.5 1.0 CD2 A:HIS491 4.1 30.6 1.0 OD1 A:ASP386 4.8 50.1 1.0 CG A:ASP386 4.8 47.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Crosslink Stabilized Long-Form PDE4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:39.9 occ:1.00 O B:HOH1039 1.9 59.4 1.0 NE2 B:HIS410 2.0 38.5 1.0 NE2 B:HIS446 2.0 35.2 1.0 OD2 B:ASP447 2.2 47.3 1.0 OD1 B:ASP564 2.2 44.6 1.0 CD2 B:HIS446 2.9 34.6 1.0 CE1 B:HIS410 3.0 38.8 1.0 CD2 B:HIS410 3.0 38.4 1.0 CE1 B:HIS446 3.0 35.2 1.0 CG B:ASP564 3.1 42.6 1.0 CG B:ASP447 3.2 42.7 1.0 OD2 B:ASP564 3.3 43.0 1.0 OD1 B:ASP447 3.8 44.2 1.0 O B:HOH1020 3.8 54.0 1.0 MG B:MG803 3.9 65.6 1.0 CG B:HIS446 4.1 32.5 1.0 ND1 B:HIS446 4.1 34.6 1.0 CG B:HIS410 4.1 37.8 1.0 ND1 B:HIS410 4.1 40.0 1.0 CD2 B:HIS406 4.2 36.1 1.0 CB B:ASP447 4.4 32.8 1.0 CG2 B:VAL414 4.4 34.1 1.0 CB B:ASP564 4.4 39.3 1.0 O B:HOH948 4.5 39.8 1.0 NE2 B:HIS406 4.6 36.5 1.0 O B:HOH1040 4.7 54.1 1.0 CA B:ASP564 5.0 40.5 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.