Sodium in PDB 5tfl: Crystal Structure of Mouse Cadherin-23 EC7+8

The structure of Crystal Structure of Mouse Cadherin-23 EC7+8, PDB code: 5tfl 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)	131.39 / 3.56
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	185.809, 185.809, 185.809, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.1

The structure of Crystal Structure of Mouse Cadherin-23 EC7+8 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Mouse Cadherin-23 EC7+8 (pdb code 5tfl). 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 Mouse Cadherin-23 EC7+8, PDB code: 5tfl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mouse Cadherin-23 EC7+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 Mouse Cadherin-23 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:71.1 occ:1.00 OD1 A:ASP712 2.3 84.2 1.0 OD2 A:ASP750 2.6 87.3 1.0 OE2 A:GLU714 2.9 69.2 1.0 OE1 A:GLU659 2.9 75.1 1.0 CG A:ASP750 3.2 85.6 1.0 OD1 A:ASP750 3.3 85.1 1.0 CG A:ASP712 3.4 82.1 1.0 ND2 A:ASN751 3.7 75.6 1.0 OD2 A:ASP712 4.0 81.5 1.0 CD A:GLU659 4.0 75.1 1.0 CD A:GLU714 4.1 70.6 1.0 O A:HOH1002 4.1 44.1 1.0 O A:ASP750 4.3 75.7 1.0 CB A:ASP750 4.4 82.5 1.0 OE2 A:GLU659 4.5 78.7 1.0 CB A:ASP712 4.5 80.7 1.0 CG A:ASN751 4.6 73.3 1.0 CA A:CA902 4.6 58.9 1.0 OD1 A:ASN751 4.7 76.0 1.0 CG A:GLU714 4.8 75.1 1.0 C A:ASP750 4.9 73.1 1.0 CA A:ASP712 5.0 78.0 1.0 OE1 A:GLU714 5.0 67.2 1.0 CB A:GLU714 5.0 75.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mouse Cadherin-23 EC7+8


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 Mouse Cadherin-23 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:95.8 occ:1.00 OD1 B:ASP712 2.4 0.8 1.0 OE2 B:GLU714 2.7 90.9 1.0 OD2 B:ASP750 2.7 0.3 1.0 OE2 B:GLU659 3.1 94.3 1.0 CG B:ASP750 3.2 97.4 1.0 OD1 B:ASP750 3.2 95.3 1.0 CG B:ASP712 3.4 0.1 1.0 ND2 B:ASN751 3.5 90.8 1.0 CD B:GLU714 4.0 89.9 1.0 OD2 B:ASP712 4.0 0.3 1.0 CD B:GLU659 4.1 95.1 1.0 OE1 B:GLU659 4.2 95.6 1.0 O B:ASP750 4.2 0.7 1.0 CB B:ASP750 4.4 97.8 1.0 CG B:ASN751 4.4 92.0 1.0 OD1 B:ASN751 4.5 97.8 1.0 CB B:ASP712 4.6 0.1 1.0 CG B:GLU714 4.7 90.5 1.0 C B:ASP750 4.8 96.6 1.0 CA B:CA902 4.8 81.1 1.0 CB B:GLU714 4.8 91.4 1.0 OE1 B:GLU714 4.9 87.8 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