Sodium in PDB 5vh2: Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D

The structure of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D, PDB code: 5vh2 was solved by D.J.Termine, A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.99 / 2.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.738, 47.210, 113.044, 89.95, 90.02, 115.76
R / Rfree (%)	23.8 / 27.2

The structure of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Sodium atom in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D (pdb code 5vh2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D, PDB code: 5vh2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D


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 EC12-13 with Engineered Mutation S1339D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1404 b:28.7 occ:1.00 OD1 A:ASP1316 2.1 27.9 1.0 O A:ALA1287 2.2 27.5 1.0 O A:GLU1286 2.4 30.4 1.0 OD2 A:ASP1370 2.5 29.6 1.0 OD2 A:ASP1318 2.7 30.9 1.0 C A:GLU1286 3.1 30.5 1.0 C A:ALA1287 3.3 27.5 1.0 CG A:ASP1316 3.3 27.7 1.0 CG A:ASP1370 3.6 29.3 1.0 CG A:ASP1318 3.7 31.3 1.0 N A:ALA1287 3.7 29.7 1.0 N A:ASP1318 3.8 28.3 1.0 N A:ILE1317 3.8 26.2 1.0 CA A:ALA1287 3.8 28.7 1.0 CB A:ASP1370 4.0 28.3 1.0 CB A:ASP1318 4.1 30.5 1.0 CA A:GLU1286 4.1 31.7 1.0 CG2 A:VAL1288 4.1 26.1 1.0 OD2 A:ASP1316 4.1 28.5 1.0 CA A:ASP1316 4.2 25.7 1.0 CB A:ASP1316 4.2 26.5 1.0 CB A:GLU1286 4.3 31.0 1.0 C A:ASP1316 4.3 25.9 1.0 CD1 A:LEU1284 4.3 32.1 1.0 N A:GLU1286 4.3 32.9 1.0 N A:VAL1288 4.4 26.6 1.0 CB A:ILE1317 4.5 27.2 1.0 CA A:ILE1317 4.5 26.6 1.0 CA A:ASP1318 4.6 29.4 1.0 OD1 A:ASP1370 4.6 29.9 1.0 C A:ILE1317 4.6 27.5 1.0 CA A:VAL1288 4.7 25.6 1.0 OD1 A:ASP1318 4.8 32.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D


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 EC12-13 with Engineered Mutation S1339D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1404 b:26.8 occ:1.00 OD2 B:ASP1370 1.9 25.7 1.0 O B:GLU1286 2.2 28.3 1.0 OD1 B:ASP1316 2.4 26.4 1.0 OD2 B:ASP1318 2.6 29.3 1.0 O B:ALA1287 2.8 26.8 1.0 CG B:ASP1370 3.0 24.8 1.0 C B:GLU1286 3.2 29.3 1.0 CG B:ASP1316 3.5 26.0 1.0 CB B:ASP1370 3.6 24.0 1.0 C B:ALA1287 3.7 26.8 1.0 CG B:ASP1318 3.7 30.3 1.0 CD1 B:LEU1284 3.8 20.7 1.0 N B:ALA1287 4.0 29.0 1.0 OD1 B:ASP1370 4.0 24.7 1.0 CA B:ALA1287 4.0 27.7 1.0 CA B:GLU1286 4.2 31.0 1.0 CG2 B:VAL1288 4.2 24.2 1.0 N B:GLU1286 4.2 31.3 1.0 CB B:ASP1318 4.2 29.7 1.0 OD2 B:ASP1316 4.2 26.4 1.0 N B:ASP1318 4.3 29.2 1.0 CG B:LEU1284 4.4 20.8 1.0 N B:ILE1317 4.5 27.2 1.0 CB B:GLU1286 4.6 31.5 1.0 CB B:ASP1316 4.6 25.3 1.0 CA B:ASP1316 4.7 25.4 1.0 N B:VAL1288 4.7 26.1 1.0 OD1 B:ASP1318 4.8 31.8 1.0 C B:ASP1316 4.9 26.6 1.0 CA B:ASP1318 4.9 30.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1403 b:16.4 occ:1.00 OD2 C:ASP1370 2.2 17.7 1.0 O C:ALA1287 2.2 15.3 1.0 O C:GLU1286 2.3 17.1 1.0 OD1 C:ASP1316 2.3 15.9 1.0 OD2 C:ASP1318 2.6 16.9 1.0 C C:GLU1286 3.1 16.7 1.0 C C:ALA1287 3.2 15.4 1.0 CG C:ASP1370 3.4 18.1 1.0 CG C:ASP1316 3.6 16.0 1.0 N C:ALA1287 3.6 16.2 1.0 CA C:ALA1287 3.7 16.1 1.0 CG C:ASP1318 3.7 16.7 1.0 N C:ASP1318 4.0 15.0 1.0 CG2 C:VAL1288 4.0 15.8 1.0 CB C:ASP1370 4.0 17.8 1.0 N C:ILE1317 4.0 14.3 1.0 CA C:GLU1286 4.1 16.9 1.0 CD1 C:LEU1284 4.2 17.9 1.0 CB C:ASP1318 4.2 16.4 1.0 N C:GLU1286 4.3 17.8 1.0 N C:VAL1288 4.3 15.1 1.0 OD2 C:ASP1316 4.3 16.6 1.0 CB C:GLU1286 4.3 16.0 1.0 OD1 C:ASP1370 4.4 18.9 1.0 CA C:ASP1316 4.5 14.8 1.0 CB C:ASP1316 4.5 15.6 1.0 C C:ASP1316 4.6 14.4 1.0 CB C:ILE1317 4.6 14.1 1.0 CA C:VAL1288 4.7 14.7 1.0 CA C:ILE1317 4.7 14.0 1.0 CA C:ASP1318 4.8 15.5 1.0 CG C:LEU1284 4.8 17.3 1.0 OD1 C:ASP1318 4.8 16.9 1.0 C C:ILE1317 4.9 14.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Mouse Cadherin-23 EC12-13 with Engineered Mutation S1339D within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1403 b:28.7 occ:1.00 OD2 D:ASP1370 2.2 28.5 1.0 O D:GLU1286 2.3 29.1 1.0 OD2 D:ASP1318 2.3 29.6 1.0 OD1 D:ASP1316 2.4 28.2 1.0 O D:ALA1287 2.7 27.9 1.0 C D:GLU1286 3.1 29.3 1.0 CG D:ASP1370 3.4 28.2 1.0 CG D:ASP1318 3.4 29.9 1.0 CG D:ASP1316 3.5 28.1 1.0 C D:ALA1287 3.6 27.9 1.0 CD1 D:LEU1284 3.7 24.1 1.0 N D:ALA1287 3.9 28.9 1.0 CB D:ASP1318 3.9 29.6 1.0 N D:ASP1318 4.0 28.7 1.0 CA D:GLU1286 4.0 29.9 1.0 CA D:ALA1287 4.0 28.3 1.0 CB D:ASP1370 4.0 27.9 1.0 N D:GLU1286 4.1 30.4 1.0 OD2 D:ASP1316 4.2 28.5 1.0 CB D:GLU1286 4.3 29.8 1.0 OD1 D:ASP1370 4.3 28.3 1.0 N D:ILE1317 4.4 27.6 1.0 CG D:LEU1284 4.4 24.3 1.0 CG2 D:VAL1288 4.4 27.1 1.0 OD1 D:ASP1318 4.5 30.5 1.0 CA D:ASP1318 4.6 29.3 1.0 CB D:ASP1316 4.6 27.5 1.0 CA D:ASP1316 4.7 27.2 1.0 N D:VAL1288 4.7 27.4 1.0 C D:ASP1316 4.8 27.4 1.0 CB D:ILE1317 4.9 28.2 1.0 CA D:ILE1317 5.0 27.9 1.0 C D:ILE1317 5.0 28.4 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