Sodium 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
Iodine	(I)	2 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na803 b:63.0 occ:1.00 O A:HOH952 2.5 32.2 1.0 O A:TYR399 2.8 32.7 1.0 O A:HOH1052 2.8 60.4 1.0 OG A:SER401 2.9 53.1 1.0 O A:ASP397 3.3 32.9 1.0 O A:HOH1010 3.8 52.3 1.0 N A:SER401 3.9 33.4 1.0 O A:GLU396 3.9 30.4 1.0 C A:ASP397 4.0 32.5 1.0 C A:TYR399 4.0 30.9 1.0 CA A:ASP397 4.1 28.6 1.0 CB A:SER401 4.1 36.8 1.0 O A:HOH1037 4.3 46.1 1.0 O A:HOH959 4.5 32.1 1.0 C A:HIS400 4.5 34.2 1.0 CA A:SER401 4.5 33.7 1.0 CA A:HIS400 4.6 26.2 1.0 N A:HIS400 4.8 26.5 1.0 C A:GLU396 4.8 30.4 1.0 N A:TYR399 4.8 24.3 1.0 N A:ASP397 4.9 27.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na802 b:61.8 occ:1.00 O B:HOH993 2.5 34.5 1.0 O B:TYR399 2.7 39.7 1.0 O B:HOH941 2.7 48.1 1.0 O B:ASP397 3.1 38.8 1.0 OG B:SER401 3.1 63.3 1.0 O B:HOH978 3.7 59.6 1.0 C B:ASP397 3.8 37.7 1.0 N B:SER401 3.8 45.0 1.0 C B:TYR399 3.9 39.0 1.0 CA B:ASP397 4.0 35.2 1.0 O B:GLU396 4.1 34.6 1.0 CB B:SER401 4.3 50.0 1.0 OD1 B:ASP397 4.3 65.6 1.0 CA B:HIS400 4.4 38.0 1.0 C B:HIS400 4.4 47.1 1.0 CA B:SER401 4.6 46.4 1.0 N B:HIS400 4.6 37.8 1.0 N B:TYR399 4.7 32.2 1.0 O B:HOH995 4.8 39.4 1.0 N B:HIS398 4.9 33.9 1.0 C B:GLU396 4.9 36.7 1.0 N B:ASP397 4.9 34.5 1.0 CA B:TYR399 4.9 32.8 1.0 CG B:ASP397 5.0 64.6 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.