Sodium in PDB 5k8r: Structure of Human Clustered Protocadherin Gamma B3 EC1-4

The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r was solved by J.M.Nicoludis, B.E.Vogt, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.35 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	128.881, 161.229, 53.659, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.9

The structure of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	9 atoms

The binding sites of Sodium atom in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4 (pdb code 5k8r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4, PDB code: 5k8r:

Sodium binding site 1 out of 1 in the Structure of Human Clustered Protocadherin Gamma B3 EC1-4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Clustered Protocadherin Gamma B3 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na512 b:73.6 occ:1.00 O A:GLU328 2.5 57.7 1.0 O A:LEU380 2.5 46.9 1.0 C A:GLU328 3.1 47.9 1.0 C A:LEU380 3.6 40.8 1.0 N A:ASP329 3.6 47.5 1.0 CA A:ASP329 3.7 49.2 1.0 CB A:GLU328 3.8 35.0 1.0 CG A:GLU328 3.9 47.6 1.0 CA A:GLU328 4.0 37.1 1.0 CD A:GLU328 4.4 58.1 1.0 CB A:ASP329 4.4 49.0 1.0 CA A:LEU380 4.4 34.4 1.0 N A:LEU380 4.5 37.4 1.0 CB A:LEU380 4.5 33.1 1.0 N A:ASP381 4.5 40.2 1.0 OE1 A:GLU328 4.6 58.3 1.0 CA A:ASP381 4.7 46.0 1.0 C A:ASP329 4.9 45.3 1.0

J.M.Nicoludis, B.E.Vogt, A.G.Green, C.P.Scharfe, D.S.Marks, R.Gaudet. Antiparallel Protocadherin Homodimers Use Distinct Affinity- and Specificity-Mediating Regions in Cadherin Repeats 1-4. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27472898
DOI: 10.7554/ELIFE.18449