Calcium in PDB 2wcp: Crystal Structure of Mouse Cadherin-23 EC1-2

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2, PDB code: 2wcp was solved by M.Sotomayor, W.Weihofen, R.Gaudet, D.P.Corey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.98
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	151.463, 151.463, 133.457, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 18.8

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC1-2 (pdb code 2wcp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC1-2, PDB code: 2wcp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Mouse Cadherin-23 EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:16.6 occ:1.00 O A:ARG5 2.2 20.1 1.0 OD2 A:ASP41 2.3 18.1 1.0 OD2 A:ASP87 2.3 23.7 1.0 OD1 A:ASP37 2.4 16.2 1.0 OD1 A:ASN4 2.5 21.9 1.0 OD2 A:ASP39 2.5 17.6 1.0 OD2 A:ASP37 2.6 19.4 1.0 CG A:ASP37 2.8 19.2 1.0 CG A:ASP41 3.4 18.1 1.0 C A:ARG5 3.4 20.6 1.0 CG A:ASN4 3.4 24.7 1.0 CG A:ASP87 3.4 25.3 1.0 CG A:ASP39 3.5 18.0 1.0 ND2 A:ASN4 3.7 22.4 1.0 CB A:ASP39 3.8 18.3 1.0 CB A:ASP87 3.8 25.9 1.0 CB A:ASP41 4.0 18.4 1.0 N A:ARG5 4.0 22.4 1.0 CA A:ARG5 4.2 21.2 1.0 N A:LEU6 4.3 19.5 1.0 OE1 A:GLN89 4.3 20.4 0.5 O A:HOH2007 4.3 31.8 1.0 OD1 A:ASP41 4.3 17.7 1.0 CB A:ASP37 4.4 18.4 1.0 CA A:LEU6 4.4 19.1 1.0 OD1 A:ASP87 4.6 23.2 1.0 OD1 A:ASP39 4.6 17.1 1.0 C A:LEU6 4.7 18.0 1.0 CB A:ASN4 4.7 25.4 1.0 N A:ASP39 4.7 19.7 1.0 CB A:ARG5 4.8 20.7 1.0 C A:ASN4 4.8 23.7 1.0 CD A:PRO7 4.8 17.4 1.0 CA A:ASP39 4.9 18.9 1.0 N A:PRO7 4.9 17.4 1.0 CD A:GLN89 4.9 25.6 0.5 NE2 A:GLN89 5.0 19.9 0.5 CA A:ASN4 5.0 25.7 1.0

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


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:10.9 occ:1.00 OE1 A:GLU22 2.3 10.9 1.0 OD1 A:ASP138 2.3 15.2 1.0 OD1 A:ASP102 2.3 11.9 1.0 OE1 A:GLU74 2.3 18.9 1.0 OD1 A:ASP105 2.4 11.6 1.0 O A:VAL103 2.4 11.3 1.0 OE2 A:GLU74 2.5 15.9 1.0 CD A:GLU74 2.8 15.9 1.0 CD A:GLU22 3.4 14.9 1.0 CG A:ASP102 3.4 13.3 1.0 CG A:ASP105 3.5 13.3 1.0 CG A:ASP138 3.5 18.2 1.0 C A:VAL103 3.6 12.2 1.0 NA A:NA501 3.7 13.4 1.0 OE2 A:GLU22 3.7 11.4 1.0 N A:VAL103 3.8 12.2 1.0 OD1 A:ASN106 3.9 14.1 1.0 OD2 A:ASP102 3.9 14.4 1.0 OD2 A:ASP105 4.0 14.1 1.0 N A:ASP105 4.1 13.0 1.0 CB A:ASP138 4.2 18.6 1.0 CG A:GLU74 4.2 17.0 1.0 CA A:ASP138 4.3 18.9 1.0 CA A:VAL103 4.4 11.5 0.5 CA A:VAL103 4.4 12.2 0.5 OD2 A:ASP138 4.4 15.4 1.0 NE A:ARG73 4.5 17.4 1.0 CB A:ASP102 4.5 12.5 1.0 CA A:ASP102 4.6 12.2 1.0 N A:ASN104 4.6 12.5 1.0 CB A:ASP105 4.6 13.1 1.0 CG A:GLU22 4.7 12.6 1.0 C A:ASP102 4.7 12.5 1.0 CG2 A:VAL103 4.7 8.3 0.5 CA A:ASN104 4.7 12.9 1.0 NH1 A:ARG73 4.8 18.5 1.0 CA A:ASP105 4.8 12.8 1.0 C A:ASN104 4.9 13.1 1.0 CB A:ARG73 4.9 16.0 1.0

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


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:12.1 occ:1.00 O A:GLY142 2.3 18.4 1.0 O A:ASN106 2.3 11.8 1.0 OD2 A:ASP136 2.4 18.6 1.0 OD1 A:ASN104 2.4 13.5 1.0 OD2 A:ASP138 2.4 15.4 1.0 OD1 A:ASP136 2.4 18.6 1.0 OD2 A:ASP187 2.6 18.9 1.0 CG A:ASP136 2.7 20.1 1.0 CG A:ASP138 3.4 18.2 1.0 C A:GLY142 3.4 18.9 1.0 CG A:ASP187 3.4 18.0 1.0 CG A:ASN104 3.5 13.1 1.0 C A:ASN106 3.5 12.2 1.0 CB A:ASP138 3.7 18.6 1.0 CB A:ASP187 3.7 18.2 1.0 ND2 A:ASN104 4.0 12.1 1.0 N A:ASN106 4.2 12.2 1.0 CA A:GLY142 4.2 19.5 1.0 CA A:ASN106 4.2 12.7 1.0 CB A:ASP136 4.2 20.1 1.0 CB A:ASN106 4.3 12.1 1.0 N A:GLY143 4.4 18.6 1.0 OD1 A:ASP187 4.5 18.0 1.0 N A:ALA107 4.5 13.7 1.0 OD1 A:ASP138 4.6 15.2 1.0 CA A:GLY143 4.6 19.3 1.0 N A:ASP138 4.7 18.3 1.0 CA A:ALA107 4.7 13.9 1.0 CB A:ASN104 4.7 13.0 1.0 CD1 A:LEU194 4.8 28.6 1.0 CA A:ASP138 4.8 18.9 1.0 CA A:ASN104 4.9 12.9 1.0 CB A:LEU194 4.9 29.0 1.0 C A:ALA107 5.0 14.4 1.0

M.Sotomayor, W.Weihofen, R.Gaudet, D.P.Corey. Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Neuron V. 66 85 2010.
ISSN: ISSN 0896-6273
PubMed: 20399731
DOI: 10.1016/J.NEURON.2010.03.028