Calcium in PDB 5wj8: Crystal Structure of Human Cadherin-23 EC13-14

The structure of Crystal Structure of Human Cadherin-23 EC13-14, PDB code: 5wj8 was solved by F.Velez-Cortes, C.Conghui, P.De-La-Torre, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.17 / 1.86
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.712, 74.712, 213.507, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 24.8

The structure of Crystal Structure of Human Cadherin-23 EC13-14 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Cadherin-23 EC13-14 (pdb code 5wj8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Cadherin-23 EC13-14, PDB code: 5wj8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Cadherin-23 EC13-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Cadherin-23 EC13-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1601 b:48.8 occ:1.00 O A:HOH1785 2.3 41.1 1.0 O A:LYS1374 2.3 53.8 1.0 O A:GLY1372 2.3 47.1 1.0 OD1 A:ASP1370 2.3 48.1 1.0 O A:HOH1736 2.4 43.7 1.0 OD2 A:ASP1376 2.5 50.7 1.0 OD1 A:ASP1376 2.6 50.3 1.0 CG A:ASP1376 2.9 50.2 1.0 C A:GLY1372 3.4 48.3 1.0 CG A:ASP1370 3.5 47.5 1.0 C A:LYS1374 3.5 55.7 1.0 N A:GLY1372 3.7 44.6 1.0 N A:LYS1374 4.0 55.4 1.0 OD2 A:ASP1370 4.1 49.5 1.0 CA A:GLY1372 4.2 46.5 1.0 C A:PRO1373 4.2 54.7 1.0 N A:GLY1371 4.2 42.0 1.0 OD1 A:ASP1369 4.2 42.8 1.0 CB A:ASP1376 4.3 49.6 1.0 CA A:LYS1374 4.3 56.8 1.0 N A:ASP1370 4.3 42.6 1.0 N A:ASP1376 4.4 52.3 1.0 N A:PRO1373 4.4 51.2 1.0 O A:HOH1739 4.5 44.0 1.0 N A:VAL1375 4.5 56.5 1.0 CB A:ASP1370 4.6 45.0 1.0 CA A:PRO1373 4.6 53.5 1.0 C A:VAL1375 4.6 54.1 1.0 O A:PRO1373 4.6 56.3 1.0 C A:GLY1371 4.7 43.8 1.0 CA A:ASP1370 4.7 42.9 1.0 C A:ASP1370 4.7 42.3 1.0 O A:HOH1704 4.7 46.4 1.0 CA A:VAL1375 4.7 56.3 1.0 CA A:ASP1376 4.8 50.6 1.0 O A:HOH1808 4.8 49.1 1.0 CB A:LYS1374 4.8 57.7 1.0 CA A:GLY1371 4.9 42.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Cadherin-23 EC13-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Cadherin-23 EC13-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1602 b:37.1 occ:1.00 OE1 A:GLU1357 2.2 38.7 1.0 O A:HOH1802 2.3 36.4 1.0 O A:HOH1719 2.3 38.2 1.0 OD1 A:ASP1355 2.3 40.5 1.0 OE2 A:GLU1301 2.4 37.9 1.0 OD2 A:ASP1390 2.4 43.0 1.0 CG A:ASP1390 3.2 42.2 1.0 OD1 A:ASP1390 3.2 41.4 1.0 CD A:GLU1301 3.3 37.8 1.0 CG A:ASP1355 3.3 41.2 1.0 CD A:GLU1357 3.4 39.7 1.0 OE1 A:GLU1301 3.6 37.7 1.0 CA A:CA1603 4.0 37.0 1.0 OD2 A:ASP1355 4.0 42.5 1.0 O A:HOH1742 4.1 48.2 1.0 CG A:GLU1357 4.2 41.5 1.0 N A:ARG1356 4.2 38.5 1.0 CB A:ASP1355 4.2 39.8 1.0 CA A:ASP1355 4.2 38.7 1.0 N A:GLU1357 4.3 40.9 1.0 CB A:GLU1357 4.3 41.9 1.0 OD1 A:ASN1302 4.3 38.6 1.0 OE2 A:GLU1357 4.3 39.1 1.0 ND2 A:ASN1391 4.4 41.4 1.0 ND2 A:ASN1302 4.4 38.5 1.0 C A:ASP1355 4.5 38.6 1.0 CG A:GLU1301 4.6 37.0 1.0 CB A:ASP1390 4.6 41.9 1.0 CG A:ASN1302 4.8 38.7 1.0 CA A:GLU1357 4.9 42.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Cadherin-23 EC13-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Cadherin-23 EC13-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1603 b:37.0 occ:1.00 OE1 A:GLU1301 2.2 37.7 1.0 OD1 A:ASP1390 2.3 41.4 1.0 OD1 A:ASP1424 2.4 42.4 1.0 OD1 A:ASP1387 2.4 46.9 1.0 O A:GLU1388 2.4 43.0 1.0 OE2 A:GLU1357 2.5 39.1 1.0 OE1 A:GLU1357 2.7 38.7 1.0 CD A:GLU1357 2.9 39.7 1.0 CG A:ASP1424 3.4 42.3 1.0 CD A:GLU1301 3.4 37.8 1.0 CG A:ASP1390 3.4 42.2 1.0 CG A:ASP1387 3.5 46.7 1.0 C A:GLU1388 3.6 44.3 1.0 OE2 A:GLU1301 3.8 37.9 1.0 N A:GLU1388 3.9 46.6 1.0 OD2 A:ASP1387 3.9 46.2 1.0 CA A:CA1602 4.0 37.1 1.0 CB A:ASP1424 4.0 43.1 1.0 OD2 A:ASP1390 4.0 43.0 1.0 ND2 A:ASN1391 4.1 41.4 1.0 N A:ASP1390 4.1 41.0 1.0 CA A:ASP1424 4.2 44.2 1.0 CA A:GLU1388 4.3 45.9 1.0 OD2 A:ASP1424 4.3 41.4 1.0 CG A:GLU1357 4.4 41.5 1.0 NE A:ARG1356 4.4 43.0 1.0 CB A:ASP1390 4.6 41.9 1.0 CB A:ASP1387 4.6 48.4 1.0 CG A:GLU1301 4.6 37.0 1.0 CA A:ASP1387 4.6 48.9 1.0 N A:ASN1389 4.7 43.4 1.0 C A:ASP1387 4.7 47.7 1.0 CB A:GLU1388 4.8 46.8 1.0 CA A:ASP1390 4.8 40.8 1.0 CB A:ARG1356 4.9 40.1 1.0 CA A:ASN1389 4.9 42.2 1.0 O A:HOH1802 4.9 36.4 1.0 NH2 A:ARG1356 4.9 45.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Cadherin-23 EC13-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Cadherin-23 EC13-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1604 b:38.8 occ:1.00 O A:ASN1391 2.3 38.3 1.0 O A:ASN1428 2.3 41.4 1.0 OD1 A:ASN1389 2.4 41.3 1.0 OD2 A:ASP1424 2.4 41.4 1.0 OD2 A:ASP1422 2.4 40.3 1.0 OD2 A:ASP1478 2.5 41.0 1.0 OD1 A:ASP1422 2.7 41.5 1.0 CG A:ASP1422 2.9 41.4 1.0 C A:ASN1391 3.4 38.7 1.0 CG A:ASP1478 3.5 42.2 1.0 CG A:ASP1424 3.5 42.3 1.0 C A:ASN1428 3.5 43.5 1.0 CG A:ASN1389 3.5 41.5 1.0 CB A:ASP1478 3.8 42.7 1.0 CB A:ASP1424 3.9 43.1 1.0 ND2 A:ASN1389 4.0 40.8 1.0 CA A:ASN1391 4.2 39.4 1.0 N A:ASN1391 4.2 39.6 1.0 CA A:ASN1428 4.3 44.4 1.0 CB A:ASN1391 4.4 39.5 1.0 CB A:ASP1422 4.4 41.6 1.0 CB A:ASN1428 4.4 44.7 1.0 N A:GLY1429 4.4 44.7 1.0 N A:SER1392 4.4 39.3 1.0 OD1 A:ASP1478 4.5 41.6 1.0 CA A:GLY1429 4.6 45.3 1.0 OD1 A:ASP1424 4.6 42.4 1.0 CA A:SER1392 4.6 39.2 1.0 CB A:ASN1389 4.7 42.3 1.0 CA A:ASN1389 4.8 42.2 1.0 CD A:ARG1484 4.8 42.4 1.0 C A:ASN1389 4.9 41.5 1.0 C A:SER1392 4.9 39.9 1.0 CD A:PRO1393 4.9 40.4 1.0 N A:ASP1424 5.0 43.8 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