Sodium in PDB 5tfm: Crystal Structure of Human Cadherin-23 EC6-8

The structure of Crystal Structure of Human Cadherin-23 EC6-8, PDB code: 5tfm was solved by A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.89 / 2.92
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	93.407, 93.407, 122.386, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.6

The structure of Crystal Structure of Human Cadherin-23 EC6-8 also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Cadherin-23 EC6-8 (pdb code 5tfm). 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 Crystal Structure of Human Cadherin-23 EC6-8, PDB code: 5tfm:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Human Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:97.1 occ:1.00 OD1 A:ASP712 2.2 99.1 1.0 OD2 A:ASP750 2.2 95.4 1.0 O A:HOH1009 2.3 74.3 1.0 OE2 A:GLU659 2.4 83.8 1.0 OE2 A:GLU714 2.7 94.1 1.0 CG A:ASP750 3.2 94.3 1.0 CG A:ASP712 3.3 0.2 1.0 OD1 A:ASP750 3.4 91.8 1.0 CD A:GLU659 3.5 85.4 1.0 CA A:ASP712 3.7 98.7 1.0 CB A:ASP712 3.9 0.4 1.0 CD A:GLU714 3.9 89.5 1.0 N A:ARG713 4.0 88.8 1.0 OE1 A:GLU659 4.2 83.3 1.0 C A:ASP712 4.2 91.7 1.0 OD2 A:ASP712 4.4 0.4 1.0 N A:GLU714 4.4 89.5 1.0 CA A:CA905 4.5 87.8 1.0 ND2 A:ASN751 4.5 97.0 1.0 CG A:GLU659 4.6 88.3 1.0 O A:LEU711 4.6 0.5 1.0 CB A:ASP750 4.6 95.7 1.0 CB A:GLU714 4.6 92.1 1.0 CG A:GLU714 4.7 90.3 1.0 OE1 A:GLU714 4.8 84.5 1.0 N A:ASP712 4.9 0.5 1.0

A.Jaiganesh, P.De-La-Torre, A.A.Patel, D.J.Termine, F.Velez-Cortes, C.Chen, M.Sotomayor. Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Structure V. 26 1210 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003