Calcium in PDB 5uz8: Crystal Structure of Mouse Cadherin-23 EC22-24

The structure of Crystal Structure of Mouse Cadherin-23 EC22-24, PDB code: 5uz8 was solved by A.Patel, A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.537, 57.208, 114.667, 90.00, 112.55, 90.00
R / Rfree (%)	17.1 / 18.8

The structure of Crystal Structure of Mouse Cadherin-23 EC22-24 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC22-24 (pdb code 5uz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC22-24, PDB code: 5uz8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


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 Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2604 b:13.6 occ:1.00 OD1 A:ASN2480 2.3 14.9 1.0 O A:ASN2518 2.3 15.7 1.0 O A:CYS2482 2.3 14.8 1.0 OD2 A:ASP2562 2.3 14.6 1.0 OD2 A:ASP2514 2.4 13.5 1.0 OD2 A:ASP2512 2.4 15.0 1.0 OD1 A:ASP2512 2.6 15.2 1.0 CG A:ASP2512 2.9 15.2 1.0 CG A:ASP2562 3.4 15.1 1.0 CG A:ASP2514 3.4 14.8 1.0 CG A:ASN2480 3.4 15.7 1.0 C A:CYS2482 3.5 15.8 1.0 C A:ASN2518 3.5 16.9 1.0 CB A:ASP2514 3.7 15.2 1.0 CB A:ASP2562 3.8 15.3 1.0 ND2 A:ASN2480 3.9 16.2 1.0 N A:CYS2482 4.3 16.4 1.0 CA A:CYS2482 4.3 16.8 1.0 OD1 A:ASP2562 4.4 15.1 1.0 CB A:ASP2512 4.4 15.8 1.0 CA A:ASN2518 4.4 17.4 1.0 CD1 A:LEU2568 4.4 16.1 1.0 N A:SER2519 4.4 17.9 1.0 CB A:ASN2518 4.5 17.1 1.0 CB A:CYS2482 4.5 17.9 1.0 OD1 A:ASP2514 4.5 14.9 1.0 CA A:SER2519 4.5 18.3 1.0 N A:ARG2483 4.6 15.5 1.0 CB A:ASN2480 4.7 16.2 1.0 CA A:ARG2483 4.7 15.4 1.0 N A:ASP2514 4.8 15.6 1.0 CD A:PRO2484 4.8 15.6 1.0 CA A:ASN2480 4.9 15.9 1.0 CA A:ASP2514 4.9 15.9 1.0 C A:ARG2483 5.0 15.7 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


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 Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2605 b:14.2 occ:1.00 OD1 A:ASP2514 2.3 14.9 1.0 OE2 A:GLU2390 2.3 14.8 1.0 OD1 A:ASP2478 2.3 15.8 1.0 OD1 A:ASP2481 2.4 15.5 1.0 OE1 A:GLU2443 2.4 15.4 1.0 O A:VAL2479 2.4 14.5 1.0 OE2 A:GLU2443 2.8 14.2 1.0 CD A:GLU2443 2.9 14.4 1.0 CD A:GLU2390 3.4 15.4 1.0 CG A:ASP2478 3.4 16.6 1.0 CG A:ASP2514 3.4 14.8 1.0 CG A:ASP2481 3.5 16.1 1.0 C A:VAL2479 3.6 16.0 1.0 OE1 A:GLU2390 3.8 15.5 1.0 N A:VAL2479 3.9 15.4 1.0 CA A:CA2606 3.9 16.2 1.0 N A:ASP2481 4.0 15.7 1.0 OD2 A:ASP2478 4.0 16.9 1.0 OD2 A:ASP2481 4.1 16.2 1.0 CB A:ASP2514 4.2 15.2 1.0 CA A:ASP2514 4.3 15.9 1.0 CG A:GLU2443 4.3 15.2 1.0 CA A:VAL2479 4.4 16.2 1.0 OD2 A:ASP2514 4.4 13.5 1.0 NE A:ARG2442 4.4 17.2 1.0 CB A:ASP2478 4.6 16.6 1.0 CA A:ASP2478 4.6 16.3 1.0 SG A:CYS2482 4.6 20.1 1.0 N A:ASN2480 4.6 15.9 1.0 CB A:ASP2481 4.7 16.2 1.0 CG A:GLU2390 4.7 15.2 1.0 CA A:ASN2480 4.7 15.9 1.0 C A:ASP2478 4.7 16.6 1.0 CA A:ASP2481 4.8 16.1 1.0 C A:ASN2480 4.8 16.2 1.0 CB A:ARG2442 4.9 16.0 1.0 NH2 A:ARG2442 4.9 19.1 1.0 CB A:VAL2479 4.9 16.9 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


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 Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2606 b:16.2 occ:1.00 OE2 A:GLU2443 2.2 14.2 1.0 OE1 A:GLU2390 2.4 15.5 1.0 OD1 A:ASP2441 2.4 15.8 1.0 OE1 A:GSH2611 2.4 22.2 1.0 OD2 A:ASP2481 2.4 16.2 1.0 O A:HOH2917 2.5 16.0 1.0 OD1 A:ASP2481 3.0 15.5 1.0 CG A:ASP2481 3.1 16.1 1.0 CG A:ASP2441 3.3 16.7 1.0 CD A:GLU2390 3.3 15.4 1.0 CD1 A:GSH2611 3.5 24.0 1.0 CD A:GLU2443 3.5 14.4 1.0 OE2 A:GLU2390 3.7 14.8 1.0 CA A:CA2605 3.9 14.2 1.0 OD2 A:ASP2441 4.0 16.9 1.0 CA A:ASP2441 4.1 16.3 1.0 CB A:ASP2441 4.2 16.7 1.0 N A:ARG2442 4.2 15.6 1.0 CG1 A:GSH2611 4.3 25.8 1.0 OE1 A:GLU2443 4.3 15.4 1.0 CG A:GLU2443 4.4 15.2 1.0 N2 A:GSH2611 4.4 22.6 1.0 N A:GLU2443 4.4 15.3 1.0 O A:HOH2839 4.4 32.9 1.0 CB A:GLU2443 4.4 15.8 1.0 O A:HOH2912 4.5 24.2 1.0 C A:ASP2441 4.5 16.1 1.0 CG A:GLU2390 4.5 15.2 1.0 CA2 A:GSH2611 4.5 22.5 1.0 CB A:ASP2481 4.5 16.2 1.0 SG A:CYS2482 4.6 20.1 1.0 O A:HOH2921 4.6 20.4 1.0 O12 A:GSH2611 4.8 30.5 1.0 CB1 A:GSH2611 4.9 27.8 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


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 Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2607 b:47.4 occ:1.00 OD2 A:ASP2299 2.3 45.1 1.0 O A:ASN2266 2.3 44.1 1.0 O A:HOH3007 2.4 40.0 1.0 O A:ASN2305 2.4 54.5 1.0 OD2 A:ASP2353 2.5 41.4 1.0 OD2 A:ASP2301 2.5 55.2 1.0 OD1 A:ASP2299 2.9 44.1 1.0 CG A:ASP2299 2.9 43.8 1.0 CG A:ASP2353 3.5 41.2 1.0 C A:ASN2266 3.5 44.3 1.0 CG A:ASP2301 3.5 57.7 1.0 C A:ASN2305 3.6 56.0 1.0 CB A:ASP2353 3.8 39.6 1.0 N A:ASN2266 4.0 50.7 1.0 CB A:ASP2301 4.0 58.7 1.0 CA A:ASN2266 4.2 47.7 1.0 O A:HOH2948 4.4 46.3 1.0 CB A:ASP2299 4.4 41.3 1.0 CA A:ASN2305 4.4 59.6 1.0 N A:GLY2306 4.5 54.4 1.0 OD1 A:ASP2353 4.5 42.2 1.0 N A:THR2267 4.5 41.4 1.0 CA A:GLY2306 4.6 51.6 1.0 CB A:ASN2305 4.6 61.5 1.0 OD1 A:ASP2301 4.6 57.7 1.0 CB A:ASN2266 4.6 47.5 1.0 CD A:PRO2268 4.8 34.7 1.0 CA A:THR2267 4.8 39.3 1.0 CD A:ARG2359 4.8 48.6 1.0 C A:ASP2265 4.8 54.9 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2608 b:13.1 occ:1.00 O A:ASN2375 2.3 13.9 1.0 OD2 A:ASP2456 2.3 13.7 1.0 OD1 A:ASN2373 2.4 17.8 1.0 OD2 A:ASP2407 2.4 13.4 1.0 O A:PHE2411 2.4 13.8 1.0 OD2 A:ASP2405 2.4 14.0 1.0 OD1 A:ASP2405 2.6 13.0 1.0 CG A:ASP2405 2.9 13.6 1.0 CG A:ASP2456 3.3 13.6 1.0 CG A:ASP2407 3.5 13.6 1.0 C A:ASN2375 3.5 14.4 1.0 CG A:ASN2373 3.5 18.2 1.0 C A:PHE2411 3.6 13.4 1.0 CB A:ASP2456 3.9 13.1 1.0 CB A:ASP2407 3.9 13.2 1.0 ND2 A:ASN2373 4.1 19.0 1.0 N A:ASN2375 4.2 14.0 1.0 CA A:ASN2375 4.2 14.5 1.0 OD1 A:ASP2456 4.3 14.1 1.0 CB A:ASP2405 4.4 12.9 1.0 CA A:PHE2411 4.4 14.0 1.0 CB A:ASN2375 4.4 13.7 1.0 CB A:PHE2411 4.5 13.9 1.0 N A:ASN2376 4.5 15.6 1.0 N A:ALA2412 4.5 13.6 1.0 OD1 A:ASP2407 4.6 13.9 1.0 CA A:ALA2412 4.6 13.3 1.0 CA A:ASN2376 4.7 15.8 1.0 CB A:ASN2373 4.7 17.4 1.0 CA A:ASN2373 4.8 16.4 1.0 C A:ASN2376 4.8 15.4 1.0 CD A:ARG2466 4.8 19.7 1.0 N A:ASP2407 4.8 13.4 1.0 C A:ASN2373 4.9 16.5 1.0 CD A:PRO2377 4.9 14.8 1.0 N A:PRO2377 5.0 14.4 1.0 CA A:ASP2407 5.0 13.8 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2609 b:14.3 occ:1.00 OD1 A:ASP2371 2.2 15.4 1.0 OD1 A:ASP2407 2.3 13.9 1.0 OE1 A:GLU2284 2.3 14.7 1.0 OD1 A:ASP2374 2.4 15.8 1.0 O A:ILE2372 2.5 14.9 1.0 OE1 A:GLU2340 2.5 16.8 1.0 OE2 A:GLU2340 2.6 16.4 1.0 CD A:GLU2340 2.9 17.4 1.0 CG A:ASP2407 3.4 13.6 1.0 CD A:GLU2284 3.4 14.4 1.0 CG A:ASP2371 3.5 15.9 1.0 CG A:ASP2374 3.5 16.0 1.0 C A:ILE2372 3.7 15.1 1.0 OE2 A:GLU2284 3.8 14.1 1.0 N A:ILE2372 3.8 14.4 1.0 CA A:CA2610 3.9 18.2 1.0 ND2 A:ASN2375 4.0 14.2 1.0 CB A:ASP2407 4.0 13.2 1.0 OD2 A:ASP2374 4.1 16.6 1.0 N A:ASP2374 4.1 14.2 1.0 OD2 A:ASP2371 4.2 16.6 1.0 CA A:ASP2407 4.3 13.8 1.0 OD2 A:ASP2407 4.3 13.4 1.0 CG A:GLU2340 4.4 18.3 1.0 CA A:ILE2372 4.4 14.9 1.0 CA A:ASP2371 4.5 14.5 1.0 CB A:ASP2371 4.5 15.3 1.0 CB A:TYR2339 4.6 15.0 1.0 C A:ASP2371 4.6 14.5 1.0 CB A:ASP2374 4.7 16.3 1.0 N A:ASN2373 4.7 15.5 1.0 CG1 A:ILE2372 4.7 14.6 1.0 CG A:GLU2284 4.7 14.7 1.0 CA A:ASP2374 4.8 15.4 1.0 O A:HOH2789 4.9 14.4 1.0 CD2 A:TYR2339 4.9 16.3 1.0 CA A:ASN2373 4.9 16.4 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC22-24


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Mouse Cadherin-23 EC22-24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2610 b:18.2 occ:1.00 OE2 A:GLU2340 2.3 16.4 1.0 OD1 A:ASP2338 2.4 16.8 1.0 OD2 A:ASP2374 2.4 16.6 1.0 O A:HOH2993 2.4 17.1 1.0 OE2 A:GLU2284 2.4 14.1 1.0 O A:HOH3004 2.5 17.4 1.0 CG A:ASP2374 3.1 16.0 1.0 OD1 A:ASP2374 3.1 15.8 1.0 CD A:GLU2284 3.3 14.4 1.0 CG A:ASP2338 3.4 17.5 1.0 CD A:GLU2340 3.5 17.4 1.0 OE1 A:GLU2284 3.6 14.7 1.0 CA A:CA2609 3.9 14.3 1.0 O A:HOH2831 3.9 38.5 1.0 OD2 A:ASP2338 4.0 18.4 1.0 ND2 A:ASN2375 4.1 14.2 1.0 O A:HOH2753 4.2 24.1 1.0 N A:TYR2339 4.3 15.2 1.0 N A:GLU2340 4.3 16.4 1.0 CG A:GLU2340 4.4 18.3 1.0 OE1 A:GLU2340 4.4 16.8 1.0 CA A:ASP2338 4.4 15.6 1.0 CB A:ASP2338 4.4 16.5 1.0 CB A:GLU2340 4.5 18.3 1.0 O A:HOH2752 4.5 35.4 1.0 O A:HOH2920 4.5 26.1 1.0 CB A:ASP2374 4.5 16.3 1.0 CG A:GLU2284 4.6 14.7 1.0 O A:HOH2782 4.6 21.9 1.0 O A:HOH3184 4.6 34.7 1.0 C A:ASP2338 4.7 15.6 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