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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4wzi:

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

Sodium Binding Sites:

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 4wzi

Go back to Sodium Binding Sites List in 4wzi
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 4wzi

Go back to Sodium Binding Sites List in 4wzi
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

Reference:

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.
Page generated: Tue Dec 15 09:43:23 2020

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