Sodium 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
Calcium	(Ca)	3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Mouse Cadherin-23 EC1-2, PDB code: 2wcp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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:Na501 b:13.4 occ:1.00 OE2 A:GLU74 2.3 15.9 1.0 OE2 A:GLU22 2.3 11.4 1.0 OD2 A:ASP105 2.4 14.1 1.0 OD2 A:ASP72 2.4 18.3 1.0 O A:HOH2141 2.4 18.8 1.0 OD1 A:ASP105 2.9 11.6 1.0 CG A:ASP105 3.0 13.3 1.0 CD A:GLU22 3.2 14.9 1.0 O2 A:GOL1002 3.3 60.0 1.0 CG A:ASP72 3.4 18.5 1.0 CD A:GLU74 3.5 15.9 1.0 OE1 A:GLU22 3.6 10.9 1.0 CA A:CA402 3.7 10.9 1.0 OD1 A:ASN106 4.0 14.1 1.0 N A:ARG73 4.0 14.9 1.0 CA A:ASP72 4.1 17.0 1.0 N A:GLU74 4.2 15.8 1.0 O A:HOH2174 4.2 43.1 1.0 CB A:ASP72 4.2 17.8 1.0 OD1 A:ASP72 4.3 19.0 1.0 C A:ASP72 4.3 16.3 1.0 OE1 A:GLU74 4.3 18.9 1.0 CB A:GLU74 4.3 16.0 1.0 CG A:GLU74 4.4 17.0 1.0 CB A:ASP105 4.4 13.1 1.0 O A:HOH2140 4.4 27.1 1.0 CG A:GLU22 4.5 12.6 1.0 O1 A:GOL1002 4.6 55.4 1.0 O A:HOH2173 4.6 41.3 1.0 C2 A:GOL1002 4.7 59.7 1.0 CA A:GLU74 4.9 16.3 1.0 CA A:ARG73 5.0 15.0 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na502 b:44.7 occ:1.00 O A:HOH2119 2.4 35.3 1.0 O A:HOH2105 2.4 30.9 1.0 O A:HOH2102 2.4 30.9 1.0 O A:VAL47 2.4 22.6 1.0 OG A:SER53 2.5 21.8 1.0 O A:HOH2108 2.6 36.0 1.0 CB A:SER53 3.5 23.0 1.0 C A:VAL47 3.5 22.3 1.0 O A:HOH2041 3.6 46.6 1.0 CA A:SER48 4.0 26.6 1.0 O A:HOH2104 4.0 21.3 1.0 CG1 A:VAL47 4.2 20.8 1.0 N A:SER48 4.2 24.1 1.0 O A:HOH2103 4.2 33.0 1.0 O A:HOH2042 4.3 39.0 1.0 O A:HOH2136 4.4 25.2 1.0 O A:HOH2111 4.6 47.5 1.0 N A:GLY49 4.6 26.4 1.0 CA A:VAL47 4.6 21.0 1.0 C A:SER48 4.6 26.4 1.0 CA A:SER53 4.6 22.4 1.0 O A:GLY49 4.7 26.9 1.0 O A:HOH2126 4.8 19.9 1.0 N A:VAL47 4.8 21.1 1.0 CB A:VAL47 4.9 21.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na503 b:41.4 occ:1.00 O A:HOH2214 2.3 39.1 1.0 O A:ASP136 2.4 20.7 1.0 O A:HOH2209 2.4 33.5 1.0 O A:GLY143 2.4 20.0 1.0 O A:HOH2208 2.5 23.9 1.0 O A:HOH2211 2.5 26.3 1.0 C A:GLY143 3.4 19.9 1.0 C A:ASP136 3.5 19.8 1.0 CA A:GLY143 3.8 19.3 1.0 N A:ASP136 4.0 20.8 1.0 O A:ASP138 4.2 19.4 1.0 CA A:ASP136 4.2 20.0 1.0 O A:HOH2216 4.3 26.6 1.0 O A:HOH2106 4.4 36.7 1.0 CB A:ASP136 4.4 20.1 1.0 O A:HOH2213 4.4 24.3 1.0 N A:PRO137 4.6 18.5 1.0 O A:HOH2101 4.6 24.8 1.0 N A:SER144 4.6 20.5 1.0 CA A:PRO137 4.7 18.4 1.0 O A:HOH2210 4.8 45.1 1.0 O A:HOH2206 4.9 22.4 1.0 C A:PRO137 5.0 18.4 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