Calcium in PDB 5w4t: Crystal Structure of Fish Cadherin-23 EC1-3

The structure of Crystal Structure of Fish Cadherin-23 EC1-3, PDB code: 5w4t was solved by 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)	178.05 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	178.055, 115.548, 67.895, 90.00, 89.95, 90.00
R / Rfree (%)	19.2 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Fish Cadherin-23 EC1-3 (pdb code 5w4t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 28 binding sites of Calcium where determined in the Crystal Structure of Fish Cadherin-23 EC1-3, PDB code: 5w4t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:18.9 occ:1.00 OD2 C:ASP84 2.2 18.5 1.0 OD1 C:ASN1 2.2 23.4 1.0 OD2 C:ASP34 2.3 17.1 1.0 O C:GLN2 2.4 20.7 1.0 OE2 C:GLU38 2.4 20.3 1.0 OD2 C:ASP36 2.5 20.6 1.0 OD1 C:ASP34 2.9 17.7 1.0 CG C:ASP34 3.0 17.2 1.0 CG C:ASN1 3.2 24.1 1.0 CG C:ASP84 3.4 18.3 1.0 C C:GLN2 3.5 21.9 1.0 CG C:ASP36 3.5 21.2 1.0 ND2 C:ASN1 3.6 23.6 1.0 CD C:GLU38 3.6 20.6 1.0 N C:GLN2 3.9 24.2 1.0 CB C:ASP36 4.0 20.8 1.0 OE1 C:GLU38 4.1 21.4 1.0 CB C:ASP84 4.1 17.6 1.0 CA C:GLN2 4.3 23.8 1.0 O C:HOH594 4.3 31.4 1.0 OD1 C:ASP84 4.4 18.8 1.0 N C:PRO3 4.5 21.5 1.0 CB C:ASN1 4.5 25.7 1.0 CB C:ASP34 4.5 16.8 1.0 CA C:PRO3 4.6 20.2 1.0 CD C:PRO35 4.6 19.6 1.0 OD1 C:ASP36 4.6 22.2 1.0 C C:ASN1 4.6 25.7 1.0 CD C:PRO4 4.7 17.9 1.0 C C:PRO3 4.7 19.4 1.0 N C:PRO4 4.8 18.3 1.0 CG C:GLU38 4.8 20.5 1.0 CA C:ASN1 4.8 26.6 1.0 O C:HOH511 5.0 24.4 1.0

Calcium binding site 2 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:27.8 occ:1.00 OE1 C:GLU19 2.2 26.1 1.0 OD1 C:ASP69 2.3 29.4 1.0 OE1 C:GLU71 2.3 30.5 1.0 OD2 C:ASP102 2.4 30.0 1.0 O C:HOH573 2.4 14.2 1.0 O C:HOH598 2.4 21.5 1.0 CG C:ASP102 3.2 29.9 1.0 CD C:GLU19 3.2 25.8 1.0 OD1 C:ASP102 3.2 29.3 1.0 CG C:ASP69 3.4 30.0 1.0 CD C:GLU71 3.5 30.9 1.0 OE2 C:GLU19 3.6 26.6 1.0 O C:HOH550 3.8 21.9 1.0 CA C:CA403 4.0 25.0 1.0 N C:ARG70 4.0 27.3 1.0 CA C:ASP69 4.1 27.4 1.0 OE2 C:GLU71 4.2 30.3 1.0 N C:GLU71 4.2 30.0 1.0 OD2 C:ASP69 4.2 31.3 1.0 ND2 C:ASN103 4.3 29.9 1.0 CB C:ASP69 4.3 28.8 1.0 C C:ASP69 4.4 27.6 1.0 O C:HOH592 4.4 19.7 1.0 O C:HOH577 4.4 29.3 1.0 CG C:GLU19 4.4 24.7 1.0 CB C:GLU71 4.5 32.5 1.0 O C:HOH568 4.5 21.3 1.0 CG C:GLU71 4.5 32.5 1.0 CB C:ASP102 4.6 30.8 1.0 O C:HOH569 4.7 23.3 1.0 O C:HOH618 4.8 26.8 1.0 CA C:ARG70 4.9 27.8 1.0 CB C:GLU19 5.0 23.8 1.0 CA C:GLU71 5.0 31.6 1.0

Calcium binding site 3 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:25.0 occ:1.00 OD1 C:ASP135 2.2 29.9 1.0 OD1 C:ASP99 2.3 29.2 1.0 OD1 C:ASP102 2.3 29.3 1.0 O C:VAL100 2.4 28.7 1.0 OE2 C:GLU71 2.4 30.3 1.0 OE2 C:GLU19 2.4 26.6 1.0 OE1 C:GLU71 2.8 30.5 1.0 CD C:GLU71 3.0 30.9 1.0 CG C:ASP135 3.3 29.9 1.0 CG C:ASP102 3.4 29.9 1.0 CG C:ASP99 3.4 29.3 1.0 CD C:GLU19 3.5 25.8 1.0 C C:VAL100 3.6 28.7 1.0 ND2 C:ASN103 3.8 29.9 1.0 OE1 C:GLU19 3.8 26.1 1.0 N C:VAL100 3.9 26.7 1.0 OD2 C:ASP102 3.9 30.0 1.0 CA C:CA402 4.0 27.8 1.0 OD2 C:ASP99 4.0 30.6 1.0 CB C:ASP135 4.0 30.3 1.0 N C:ASP102 4.0 30.4 1.0 OD2 C:ASP135 4.2 30.0 1.0 CA C:ASP135 4.3 30.4 1.0 CA C:VAL100 4.4 27.6 1.0 CG C:GLU71 4.4 32.5 1.0 CB C:ASP99 4.5 28.1 1.0 CB C:ASP102 4.5 30.8 1.0 N C:ASN101 4.5 32.1 1.0 CA C:ASP99 4.6 26.4 1.0 NE C:ARG70 4.7 30.8 1.0 CA C:ASN101 4.7 31.5 1.0 C C:ASP99 4.7 26.5 1.0 CA C:ASP102 4.7 30.7 1.0 CG C:GLU19 4.8 24.7 1.0 C C:ASN101 4.8 31.3 1.0 CB C:ARG70 5.0 27.8 1.0 NH2 C:ARG70 5.0 33.8 1.0 CG2 C:VAL100 5.0 27.5 1.0

Calcium binding site 4 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca404 b:29.1 occ:1.00 O C:ASN103 2.3 30.5 1.0 OD2 C:ASP184 2.4 34.9 1.0 OD2 C:ASP133 2.4 30.9 1.0 OD1 C:ASN101 2.5 31.1 1.0 O C:GLY139 2.5 30.0 1.0 OD2 C:ASP135 2.5 30.0 1.0 OD1 C:ASP133 2.5 30.5 1.0 CG C:ASP133 2.8 30.6 1.0 CG C:ASP184 3.4 36.0 1.0 CG C:ASN101 3.5 32.0 1.0 CG C:ASP135 3.5 29.9 1.0 C C:ASN103 3.5 30.5 1.0 C C:GLY139 3.7 31.1 1.0 CB C:ASP135 3.8 30.3 1.0 CB C:ASP184 3.9 35.9 1.0 ND2 C:ASN101 4.0 32.8 1.0 N C:ASN103 4.1 30.2 1.0 CA C:ASN103 4.2 30.2 1.0 OD1 C:ASP184 4.3 37.3 1.0 CB C:ASP133 4.3 30.5 1.0 CB C:ASN103 4.4 29.7 1.0 CA C:GLY139 4.4 32.5 1.0 N C:ALA104 4.5 31.1 1.0 OD1 C:ASP135 4.6 29.9 1.0 CB C:ASN101 4.7 32.5 1.0 N C:GLY140 4.7 31.4 1.0 CA C:ALA104 4.7 31.3 1.0 CA C:ASN101 4.8 31.5 1.0 C C:ALA104 4.8 30.7 1.0 CD1 C:LEU191 4.8 37.3 1.0 N C:ASP135 4.9 29.9 1.0 CA C:GLY140 4.9 30.8 1.0 N C:ASP102 4.9 30.4 1.0 CA C:ASP135 5.0 30.4 1.0

Calcium binding site 5 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca405 b:23.9 occ:1.00 OD1 C:ASP239 2.3 32.1 1.0 OD1 C:ASP203 2.4 30.4 1.0 OD1 C:ASP206 2.4 30.3 1.0 O C:ILE204 2.4 27.9 1.0 OE2 C:GLU118 2.4 26.8 1.0 OE2 C:GLU171 2.4 32.3 1.0 OE1 C:GLU171 2.9 31.1 1.0 CD C:GLU171 3.0 32.7 1.0 CD C:GLU118 3.4 26.5 1.0 CG C:ASP206 3.4 30.1 1.0 CG C:ASP239 3.5 31.2 1.0 CG C:ASP203 3.6 31.6 1.0 C C:ILE204 3.6 27.9 1.0 OE1 C:GLU118 3.8 26.9 1.0 N C:ILE204 3.9 28.5 1.0 N C:ASP206 4.0 27.5 1.0 OD2 C:ASP206 4.1 31.3 1.0 OD2 C:ASP203 4.2 32.8 1.0 CA C:CA406 4.2 30.7 1.0 CB C:ASP239 4.2 32.6 1.0 CA C:ILE204 4.3 28.0 1.0 O C:HOH510 4.4 27.4 1.0 OD2 C:ASP239 4.4 29.4 1.0 CG C:MET207 4.5 32.4 1.0 CB C:ASP206 4.5 28.7 1.0 CG C:GLU171 4.5 34.9 1.0 CA C:ASP239 4.6 34.4 1.0 N C:GLN205 4.6 29.1 1.0 CA C:ASP206 4.6 27.5 1.0 CB C:TYR170 4.6 32.7 1.0 CB C:ASP203 4.7 31.9 1.0 CA C:GLN205 4.8 27.5 1.0 CG C:GLU118 4.8 25.8 1.0 CA C:ASP203 4.8 30.2 1.0 C C:GLN205 4.8 27.1 1.0 C C:ASP203 4.8 29.4 1.0 N C:MET207 4.9 28.0 1.0 C C:ASP206 4.9 27.9 1.0 CD2 C:TYR170 5.0 35.9 1.0 CB C:ILE204 5.0 27.2 1.0

Calcium binding site 6 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca406 b:30.7 occ:1.00 O C:HOH574 2.2 18.8 1.0 OD1 C:ASP169 2.3 32.9 1.0 OD2 C:ASP206 2.3 31.3 1.0 OE1 C:GLU171 2.4 31.1 1.0 OE1 C:GLU118 2.4 26.9 1.0 CG C:ASP206 3.1 30.1 1.0 OD1 C:ASP206 3.1 30.3 1.0 CG C:ASP169 3.4 34.0 1.0 CD C:GLU118 3.5 26.5 1.0 CD C:GLU171 3.6 32.7 1.0 O C:HOH560 3.8 24.4 1.0 OE2 C:GLU118 4.0 26.8 1.0 CA C:ASP169 4.2 32.0 1.0 CA C:CA405 4.2 23.9 1.0 CB C:ASP169 4.2 33.4 1.0 OD2 C:ASP169 4.3 35.6 1.0 CB C:GLU171 4.4 35.9 1.0 CG C:GLU171 4.4 34.9 1.0 N C:TYR170 4.4 32.0 1.0 OE2 C:GLU171 4.5 32.3 1.0 N C:GLU171 4.5 34.8 1.0 CB C:ASP206 4.5 28.7 1.0 C C:ASP169 4.6 32.6 1.0 CG C:GLU118 4.7 25.8 1.0

Calcium binding site 7 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca407 b:23.3 occ:1.00 O C:MET207 2.3 26.2 1.0 OE2 C:GLU293 2.3 24.0 1.0 OD2 C:ASP239 2.3 29.4 1.0 OD1 C:ASP237 2.3 28.3 1.0 OE1 C:GLN205 2.4 25.4 1.0 O C:HOH602 2.7 23.8 1.0 OE1 C:GLU293 2.9 23.9 1.0 CD C:GLU293 3.0 23.6 1.0 CG C:ASP237 3.2 29.1 1.0 CG C:ASP239 3.5 31.2 1.0 C C:MET207 3.5 27.0 1.0 OD2 C:ASP237 3.5 29.0 1.0 CD C:GLN205 3.6 26.8 1.0 N C:MET207 4.0 28.0 1.0 CB C:ASP239 4.0 32.6 1.0 NH2 C:ARG244 4.1 25.5 1.0 CA C:MET207 4.2 28.5 1.0 NE2 C:GLN205 4.3 28.1 1.0 O A:HOH583 4.4 24.8 1.0 CG C:GLU293 4.5 23.1 1.0 OD1 C:ASP239 4.5 32.1 1.0 N C:ASP208 4.5 26.6 1.0 CB C:ASP237 4.6 30.1 1.0 CB C:GLN205 4.6 26.4 1.0 N C:ASP239 4.6 33.1 1.0 CB C:ALA303 4.6 20.2 1.0 CG C:GLN205 4.6 27.1 1.0 CB C:MET207 4.7 30.3 1.0 NE C:ARG244 4.7 27.0 1.0 CA C:GLN205 4.7 27.5 1.0 CA C:ASP208 4.7 25.6 1.0 C C:ASP208 4.8 25.9 1.0 N C:ASP206 4.8 27.5 1.0 CZ C:ARG244 4.8 26.3 1.0 C C:GLN205 4.9 27.1 1.0 CA C:ASP237 4.9 30.3 1.0 CA C:ASP239 5.0 34.4 1.0

Calcium binding site 8 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.6 occ:1.00 OE1 A:GLU38 2.3 21.5 1.0 OD2 A:ASP84 2.3 17.5 1.0 OD2 A:ASP36 2.3 21.7 1.0 O A:GLN2 2.3 18.8 1.0 OD2 A:ASP34 2.4 17.8 1.0 OD1 A:ASN1 2.4 20.0 1.0 OD1 A:ASP34 2.7 18.4 1.0 CG A:ASP34 2.9 17.8 1.0 CG A:ASN1 3.3 20.5 1.0 CD A:GLU38 3.4 21.8 1.0 CG A:ASP36 3.4 22.2 1.0 CG A:ASP84 3.4 17.6 1.0 C A:GLN2 3.5 19.8 1.0 ND2 A:ASN1 3.7 20.2 1.0 N A:GLN2 4.0 21.1 1.0 CB A:ASP84 4.0 17.2 1.0 CB A:ASP36 4.0 21.8 1.0 O A:HOH588 4.0 35.3 1.0 CG A:GLU38 4.2 21.6 1.0 OE2 A:GLU38 4.3 22.8 1.0 CA A:GLN2 4.3 21.2 1.0 CB A:ASP34 4.5 17.4 1.0 CD A:PRO4 4.5 16.9 1.0 OD1 A:ASP84 4.5 18.2 1.0 N A:PRO3 4.5 19.9 1.0 CA A:PRO3 4.5 18.9 1.0 OD1 A:ASP36 4.5 23.4 1.0 CD A:PRO35 4.5 19.8 1.0 N A:PRO4 4.6 17.2 1.0 C A:PRO3 4.6 18.1 1.0 CB A:ASN1 4.6 21.6 1.0 C A:ASN1 4.7 22.0 1.0 N A:ASP36 4.9 21.2 1.0 CA A:ASN1 4.9 22.2 1.0

Calcium binding site 9 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


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 Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:22.9 occ:1.00 OD1 A:ASP102 2.2 29.7 1.0 OD1 A:ASP99 2.3 28.4 1.0 OD1 A:ASP135 2.4 30.9 1.0 O A:VAL100 2.4 26.8 1.0 OE2 A:GLU19 2.4 25.0 1.0 OE1 A:GLU71 2.5 28.4 1.0 OE2 A:GLU71 2.8 27.8 1.0 CD A:GLU71 3.0 28.7 1.0 CG A:ASP102 3.3 30.4 1.0 CG A:ASP99 3.4 28.7 1.0 CD A:GLU19 3.4 24.2 1.0 CG A:ASP135 3.4 30.7 1.0 C A:VAL100 3.6 27.2 1.0 OE1 A:GLU19 3.7 24.7 1.0 ND2 A:ASN103 3.8 30.0 1.0 OD2 A:ASP102 3.8 30.4 1.0 CA A:CA403 3.9 26.3 1.0 OD2 A:ASP99 3.9 29.9 1.0 N A:ASP102 4.0 30.9 1.0 N A:VAL100 4.0 26.0 1.0 CB A:ASP135 4.1 31.0 1.0 OD2 A:ASP135 4.4 30.6 1.0 CA A:ASP135 4.4 31.1 1.0 CG A:GLU71 4.4 30.4 1.0 CA A:VAL100 4.4 26.8 1.0 CB A:ASP102 4.4 31.3 1.0 CB A:ASP99 4.5 27.8 1.0 N A:ASN101 4.6 32.7 1.0 CA A:ASP102 4.7 31.1 1.0 CA A:ASP99 4.7 26.1 1.0 CA A:ASN101 4.7 31.9 1.0 C A:ASN101 4.8 31.8 1.0 CG A:GLU19 4.8 23.2 1.0 C A:ASP99 4.8 26.1 1.0 NE A:ARG70 4.8 30.4 1.0 O A:HOH587 4.8 20.3 1.0 CB A:ARG70 5.0 26.9 1.0

Calcium binding site 10 out of 28 in the Crystal Structure of Fish Cadherin-23 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Fish Cadherin-23 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:26.3 occ:1.00 OE2 A:GLU71 2.2 27.8 1.0 OE1 A:GLU19 2.3 24.7 1.0 OD1 A:ASP69 2.3 28.2 1.0 O A:HOH587 2.3 20.3 1.0 OD2 A:ASP102 2.4 30.4 1.0 O A:HOH581 2.4 19.5 1.0 CG A:ASP102 3.2 30.4 1.0 OD1 A:ASP102 3.2 29.7 1.0 CD A:GLU19 3.3 24.2 1.0 CG A:ASP69 3.4 28.6 1.0 CD A:GLU71 3.5 28.7 1.0 OE2 A:GLU19 3.7 25.0 1.0 CA A:CA402 3.9 22.9 1.0 N A:ARG70 3.9 26.0 1.0 O A:HOH532 4.0 16.4 1.0 CA A:ASP69 4.1 25.9 1.0 CB A:ASP69 4.2 27.4 1.0 N A:GLU71 4.2 28.5 1.0 ND2 A:ASN103 4.2 30.0 1.0 OD2 A:ASP69 4.3 29.9 1.0 OE1 A:GLU71 4.3 28.4 1.0 C A:ASP69 4.3 26.3 1.0 O A:HOH541 4.4 21.9 1.0 O A:HOH556 4.4 27.0 1.0 CB A:GLU71 4.4 30.6 1.0 CG A:GLU71 4.4 30.4 1.0 CG A:GLU19 4.5 23.2 1.0 O A:HOH576 4.5 22.2 1.0 CB A:ASP102 4.6 31.3 1.0 CA A:ARG70 4.8 26.7 1.0 O A:HOH605 4.9 30.5 1.0 O A:HOH619 4.9 25.4 1.0 CA A:GLU71 5.0 30.1 1.0 CB A:GLU19 5.0 22.3 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