Calcium in PDB 5vt8: Crystal Structure of Mouse Cadherin-23 EC24-25

The structure of Crystal Structure of Mouse Cadherin-23 EC24-25, PDB code: 5vt8 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)	47.39 / 2.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.613, 99.387, 157.425, 90.00, 90.07, 90.00
R / Rfree (%)	20.8 / 22.1

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC24-25 (pdb code 5vt8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC24-25, PDB code: 5vt8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2801 b:39.5 occ:1.00 O B:VAL2581 2.0 42.0 1.0 OE1 B:GLU2497 2.1 38.5 1.0 OD1 B:ASP2580 2.1 39.3 1.0 OD1 B:ASP2583 2.2 37.4 1.0 OD1 B:ASP2618 2.4 35.9 1.0 C B:VAL2581 3.2 44.9 1.0 CD B:GLU2497 3.3 37.3 1.0 CG B:ASP2580 3.3 41.0 1.0 CG B:ASP2618 3.3 35.9 1.0 CG B:ASP2583 3.4 39.0 1.0 N B:VAL2581 3.5 43.3 1.0 OE2 B:GLU2497 3.8 35.4 1.0 OD2 B:ASP2583 3.9 38.9 1.0 CB B:ASP2618 3.9 35.3 1.0 CA B:VAL2581 3.9 45.3 1.0 OD2 B:ASP2580 3.9 43.3 1.0 ND2 B:ASN2584 3.9 35.3 1.0 N B:ASP2583 3.9 40.6 1.0 CA B:ASP2618 4.1 34.6 1.0 N B:ASN2582 4.3 47.5 1.0 OD2 B:ASP2618 4.3 36.2 1.0 C B:ASP2580 4.3 43.2 1.0 CB B:ASP2580 4.5 40.5 1.0 CG B:GLU2497 4.5 38.2 1.0 CA B:ASN2582 4.5 48.1 1.0 CA B:ASP2580 4.5 40.7 1.0 CB B:VAL2581 4.5 46.0 1.0 CB B:ASP2583 4.6 40.7 1.0 CA B:ASP2583 4.8 41.0 1.0 C B:ASN2582 4.8 48.9 1.0 N B:ASN2584 4.9 37.3 1.0 N B:ASP2618 4.9 34.0 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2802 b:36.6 occ:1.00 OD2 B:ASP2616 2.2 34.6 1.0 O B:ASN2622 2.2 36.8 1.0 OD2 B:ASP2618 2.3 36.2 1.0 OD2 B:ASP2672 2.4 37.3 1.0 O B:ASN2584 2.4 35.0 1.0 OD1 B:ASP2616 2.4 34.6 1.0 CG B:ASP2616 2.6 34.4 1.0 OD1 B:ASN2582 2.7 50.5 1.0 CG B:ASP2672 3.3 37.7 1.0 CG B:ASP2618 3.3 35.9 1.0 C B:ASN2622 3.4 36.6 1.0 CB B:ASP2672 3.6 36.5 1.0 C B:ASN2584 3.6 35.7 1.0 CB B:ASP2618 3.8 35.3 1.0 CG B:ASN2582 3.9 51.8 1.0 CB B:ASP2616 4.1 32.4 1.0 CA B:GLY2623 4.2 34.5 1.0 N B:GLY2623 4.2 35.2 1.0 CA B:ASN2622 4.4 37.7 1.0 OD1 B:ASP2618 4.4 35.9 1.0 OD1 B:ASP2672 4.4 40.0 1.0 CA B:ASN2584 4.5 36.1 1.0 N B:ASN2584 4.5 37.3 1.0 ND2 B:ASN2582 4.6 54.6 1.0 N B:ARG2585 4.6 35.1 1.0 CB B:ASN2622 4.6 38.0 1.0 CA B:ARG2585 4.6 35.4 1.0 CB B:ASN2584 4.6 34.6 1.0 N B:ASP2618 4.8 34.0 1.0 CD B:PRO2586 4.9 34.1 1.0 CA B:ASN2582 5.0 48.1 1.0 C B:ARG2585 5.0 33.8 1.0 CA B:ASP2618 5.0 34.6 1.0 CB B:ASN2582 5.0 51.0 1.0 CD2 B:TYR2679 5.0 42.4 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2801 b:49.1 occ:1.00 OD1 A:ASP2618 2.2 35.4 1.0 OE1 A:GLU2497 2.2 47.0 1.0 OD1 A:ASP2583 2.3 37.9 1.0 OD1 A:ASP2580 2.4 51.0 1.0 O A:VAL2581 2.5 52.7 1.0 CD A:GLU2497 3.3 45.0 1.0 CG A:ASP2618 3.3 34.8 1.0 CG A:ASP2583 3.4 41.2 1.0 ND2 A:ASN2584 3.5 36.8 1.0 CG A:ASP2580 3.6 52.8 1.0 OE2 A:GLU2497 3.6 43.0 1.0 C A:VAL2581 3.7 56.1 1.0 CB A:ASP2618 3.8 32.4 1.0 CA A:ASP2618 3.9 30.9 1.0 OD2 A:ASP2583 3.9 43.0 1.0 N A:VAL2581 4.0 53.1 1.0 N A:ASP2583 4.2 40.6 1.0 OD2 A:ASP2580 4.2 56.0 1.0 OD2 A:ASP2618 4.3 34.1 1.0 CA A:VAL2581 4.5 55.5 1.0 CG A:GLU2497 4.6 45.0 1.0 N A:ASP2618 4.6 30.2 1.0 CG A:ASN2584 4.7 35.6 1.0 CB A:ASP2583 4.7 43.1 1.0 CB A:ASP2580 4.8 51.8 1.0 N A:ASN2582 4.8 60.0 1.0 C A:ASP2580 4.8 54.0 1.0 N A:ASN2584 4.8 38.4 1.0 CA A:ASP2580 4.9 51.1 1.0 CA A:ASP2583 4.9 42.6 1.0 CA A:ASN2582 4.9 61.2 1.0 C A:ASP2618 5.0 30.2 1.0 N A:GLU2619 5.0 30.4 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2802 b:35.5 occ:1.00 OD2 A:ASP2672 2.0 33.4 1.0 O A:ASN2584 2.3 35.8 1.0 OD2 A:ASP2618 2.4 34.1 1.0 OD2 A:ASP2616 2.4 30.4 1.0 O A:ASN2622 2.4 31.9 1.0 OD1 A:ASP2616 2.8 31.1 1.0 OD1 A:ASN2582 2.9 65.2 1.0 CG A:ASP2616 3.0 30.7 1.0 CG A:ASP2672 3.0 34.0 1.0 CG A:ASN2582 3.5 66.5 1.0 CB A:ASP2672 3.5 32.2 1.0 CG A:ASP2618 3.6 34.8 1.0 C A:ASN2584 3.6 37.1 1.0 C A:ASN2622 3.6 31.0 1.0 ND2 A:ASN2582 3.7 69.5 1.0 CB A:ASP2618 4.1 32.4 1.0 OD1 A:ASP2672 4.1 35.5 1.0 N A:ASN2584 4.4 38.4 1.0 CB A:ASP2616 4.5 28.5 1.0 CA A:ARG2585 4.5 36.5 1.0 N A:ARG2585 4.5 37.0 1.0 CA A:ASN2584 4.5 37.3 1.0 CA A:ASN2622 4.5 32.0 1.0 N A:GLY2623 4.6 29.6 1.0 CD2 A:TYR2679 4.6 43.2 1.0 CA A:GLY2623 4.6 29.1 1.0 OD1 A:ASP2618 4.6 35.4 1.0 CB A:ASN2582 4.7 65.6 1.0 CA A:ASN2582 4.7 61.2 1.0 CB A:TYR2679 4.7 41.1 1.0 CB A:ASN2622 4.8 32.6 1.0 CD A:PRO2586 4.8 33.0 1.0 CB A:ASN2584 4.8 35.3 1.0 C A:ASN2582 4.9 61.1 1.0 C A:ARG2585 4.9 34.6 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2801 b:45.2 occ:1.00 O C:VAL2581 2.0 44.7 1.0 OD1 C:ASP2583 2.0 54.4 1.0 OE1 C:GLU2497 2.1 41.7 1.0 OD1 C:ASP2580 2.3 42.7 1.0 OD1 C:ASP2618 2.4 48.9 1.0 CG C:ASP2583 3.2 56.8 1.0 C C:VAL2581 3.2 45.0 1.0 CD C:GLU2497 3.3 41.0 1.0 CG C:ASP2618 3.3 49.0 1.0 CG C:ASP2580 3.5 42.5 1.0 N C:VAL2581 3.7 43.1 1.0 OD2 C:ASP2583 3.7 57.0 1.0 N C:ASP2583 3.8 57.1 1.0 OE2 C:GLU2497 3.9 39.4 1.0 CB C:ASP2618 3.9 47.6 1.0 CA C:VAL2581 4.0 44.2 1.0 ND2 C:ASN2584 4.0 52.5 1.0 OD2 C:ASP2580 4.1 43.5 1.0 CA C:ASP2618 4.2 46.2 1.0 OD2 C:ASP2618 4.2 50.2 1.0 N C:ASN2582 4.2 46.2 1.0 CB C:ASP2583 4.4 58.9 1.0 CA C:ASN2582 4.5 47.7 1.0 CG C:GLU2497 4.5 40.2 1.0 C C:ASP2580 4.5 42.5 1.0 CB C:VAL2581 4.6 45.1 1.0 CA C:ASP2583 4.6 58.1 1.0 C C:ASN2582 4.6 48.8 1.0 CB C:ASP2580 4.7 41.2 1.0 CA C:ASP2580 4.8 41.0 1.0 N C:ASN2584 4.9 54.3 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2802 b:51.6 occ:1.00 OD2 C:ASP2672 2.1 50.2 1.0 O C:ASN2622 2.2 48.8 1.0 OD1 C:ASN2582 2.3 51.0 1.0 OD2 C:ASP2616 2.3 47.5 1.0 O C:ASN2584 2.4 50.2 1.0 OD2 C:ASP2618 2.4 50.2 1.0 OD1 C:ASP2616 2.7 47.1 1.0 CG C:ASP2616 2.9 46.7 1.0 CG C:ASP2672 3.1 51.5 1.0 C C:ASN2622 3.5 48.2 1.0 CG C:ASN2582 3.5 50.8 1.0 CB C:ASP2672 3.5 50.0 1.0 CG C:ASP2618 3.6 49.0 1.0 C C:ASN2584 3.6 51.9 1.0 ND2 C:ASN2582 4.0 52.4 1.0 CB C:ASP2618 4.1 47.6 1.0 OD1 C:ASP2672 4.3 54.2 1.0 CA C:ASN2622 4.3 49.6 1.0 N C:GLY2623 4.4 46.9 1.0 CB C:ASP2616 4.4 45.6 1.0 CA C:GLY2623 4.4 45.2 1.0 N C:ASN2584 4.5 54.3 1.0 CA C:ASN2584 4.5 52.6 1.0 N C:ARG2585 4.5 52.0 1.0 CA C:ARG2585 4.6 51.3 1.0 CD2 C:TYR2679 4.6 57.3 1.0 CB C:ASN2622 4.6 50.2 1.0 OD1 C:ASP2618 4.6 48.9 1.0 CB C:ASN2582 4.7 49.2 1.0 CB C:ASN2584 4.8 50.3 1.0 CA C:ASN2582 4.8 47.7 1.0 CB C:TYR2679 4.9 56.4 1.0 CD C:PRO2586 4.9 48.6 1.0 C C:ARG2585 5.0 49.3 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


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 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2801 b:41.2 occ:1.00 OE1 D:GLU2497 1.9 36.4 1.0 OD1 D:ASP2583 2.3 60.2 1.0 O D:VAL2581 2.5 43.1 1.0 OD1 D:ASP2618 2.6 59.0 1.0 OD1 D:ASP2580 2.8 42.6 1.0 CD D:GLU2497 3.0 35.5 1.0 CG D:ASP2580 3.3 41.4 1.0 OD2 D:ASP2580 3.3 41.4 1.0 CG D:ASP2583 3.4 61.7 1.0 OE2 D:GLU2497 3.5 34.5 1.0 CG D:ASP2618 3.6 59.0 1.0 C D:VAL2581 3.7 43.0 1.0 OD2 D:ASP2583 3.7 61.9 1.0 N D:VAL2581 3.8 40.0 1.0 CB D:ASP2618 4.1 58.5 1.0 CG2 D:VAL2581 4.1 40.5 1.0 CA D:ASP2618 4.1 58.2 1.0 N D:ASP2583 4.3 62.0 1.0 CA D:VAL2581 4.3 41.2 1.0 CG D:GLU2497 4.3 34.1 1.0 OD1 D:ASN2584 4.4 63.3 1.0 CB D:ASP2580 4.5 40.5 1.0 OD2 D:ASP2618 4.6 60.1 1.0 C D:ASP2580 4.7 40.7 1.0 CB D:ASP2583 4.7 63.1 1.0 CA D:ASP2580 4.7 39.5 1.0 N D:ASN2582 4.7 44.0 1.0 CB D:VAL2581 4.9 41.1 1.0 N D:GLU2619 4.9 56.8 1.0 CA D:ASN2582 5.0 44.5 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Mouse Cadherin-23 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2802 b:58.8 occ:1.00 OD2 D:ASP2616 2.1 62.8 1.0 O D:ASN2584 2.1 63.3 1.0 OD2 D:ASP2618 2.4 60.1 1.0 O D:ASN2622 2.4 59.9 1.0 OD2 D:ASP2672 2.5 62.9 1.0 OD1 D:ASP2616 2.5 62.3 1.0 OD1 D:ASN2582 2.6 48.8 1.0 CG D:ASP2616 2.6 61.9 1.0 C D:ASN2584 3.4 64.2 1.0 CG D:ASP2672 3.4 62.8 1.0 CG D:ASP2618 3.5 59.0 1.0 C D:ASN2622 3.6 58.2 1.0 CB D:ASP2672 3.7 62.5 1.0 CG D:ASN2582 3.7 49.0 1.0 CB D:ASP2618 4.0 58.5 1.0 CB D:ASP2616 4.2 62.3 1.0 CA D:ASN2584 4.3 64.1 1.0 ND2 D:ASN2582 4.3 51.5 1.0 N D:ARG2585 4.3 65.1 1.0 CA D:GLY2623 4.4 58.8 1.0 N D:ASN2584 4.4 63.3 1.0 N D:GLY2623 4.4 58.3 1.0 CA D:ARG2585 4.4 65.0 1.0 OD1 D:ASP2618 4.5 59.0 1.0 CA D:ASN2622 4.5 57.1 1.0 CB D:ASN2584 4.5 63.4 1.0 OD1 D:ASP2672 4.6 63.3 1.0 CD2 D:TYR2679 4.7 66.1 1.0 C D:ARG2585 4.7 64.6 1.0 CB D:ASN2622 4.7 56.4 1.0 CD D:PRO2586 4.8 64.0 1.0 CB D:ASN2582 4.9 46.6 1.0 CA D:ASN2582 4.9 44.5 1.0 N D:ASP2618 5.0 59.3 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Mouse Cadherin-23 EC24-25


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Mouse Cadherin-23 EC24-25 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2803 b:42.7 occ:1.00 OD2 D:ASP2562 2.4 37.5 1.0 O D:CYS2482 2.6 39.9 1.0 OD2 D:ASP2512 3.1 37.8 1.0 CG D:ASP2562 3.5 37.7 1.0 C D:CYS2482 3.6 39.6 1.0 OD1 D:ASP2512 3.7 40.6 1.0 N D:CYS2482 3.8 41.7 1.0 CD1 D:LEU2568 3.8 37.5 1.0 CG D:ASP2512 3.8 40.0 1.0 CG D:LEU2568 3.9 37.8 1.0 OD1 D:ASP2562 4.2 38.7 1.0 CA D:CYS2482 4.3 40.8 1.0 CB D:LEU2568 4.4 36.1 1.0 N D:ASP2481 4.5 43.2 1.0 C D:ASP2481 4.5 41.6 1.0 CB D:ASP2562 4.5 37.5 1.0 N D:ARG2483 4.7 38.0 1.0 CB D:CYS2482 4.8 42.1 1.0 CA D:ARG2483 4.9 36.5 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