Sodium in PDB 2wd0: Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2

The structure of Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2, PDB code: 2wd0 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)	29.77 / 2.74
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.693, 179.693, 63.982, 90.00, 90.00, 90.00
R / Rfree (%)	21.941 / 24.865

The structure of Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	6 atoms

The binding sites of Sodium atom in the Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2 (pdb code 2wd0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2, PDB code: 2wd0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G 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 Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:29.0 occ:1.00 OD2 A:ASP105 2.1 22.4 1.0 OE2 A:GLU74 2.2 22.1 1.0 OE2 A:GLU22 2.5 21.2 1.0 OD2 A:ASP72 2.6 25.5 1.0 CG A:ASP105 3.1 20.8 1.0 OD1 A:ASP105 3.3 18.7 1.0 CD A:GLU74 3.4 22.1 1.0 CG A:ASP72 3.4 24.2 1.0 CD A:GLU22 3.5 21.0 1.0 OD1 A:ASN106 3.8 22.3 1.0 OE1 A:GLU22 4.0 21.5 1.0 CA A:ASP72 4.0 22.8 1.0 CB A:ASP72 4.1 22.9 1.0 CB A:GLU74 4.2 22.2 1.0 N A:ARG73 4.2 22.5 1.0 CG A:GLU74 4.2 22.0 1.0 OD1 A:ASP72 4.2 25.5 1.0 CA A:CA502 4.2 19.8 1.0 N A:GLU74 4.3 22.3 1.0 OE1 A:GLU74 4.3 21.2 1.0 C A:ASP72 4.4 22.6 1.0 CB A:ASP105 4.5 20.5 1.0 CG A:GLU22 4.7 20.6 1.0 CG A:ASN106 4.8 22.4 1.0 CA A:GLU74 4.9 22.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G 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 Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:26.3 occ:1.00 OE2 C:GLU74 2.1 21.7 1.0 OD2 C:ASP105 2.2 24.8 1.0 OD2 C:ASP72 2.4 25.2 1.0 OE2 C:GLU22 2.6 13.0 1.0 CG C:ASP105 3.0 22.5 1.0 CG C:ASP72 3.1 23.8 1.0 OD1 C:ASP105 3.2 22.1 1.0 CD C:GLU74 3.4 21.7 1.0 CD C:GLU22 3.5 15.4 1.0 OD1 C:ASP72 3.6 26.0 1.0 OD1 C:ASN106 3.8 26.4 1.0 OE1 C:GLU22 3.9 15.3 1.0 CA C:CA501 4.0 26.4 1.0 CB C:ASP72 4.0 21.9 1.0 CA C:ASP72 4.1 21.6 1.0 CG C:GLU74 4.1 20.8 1.0 CB C:GLU74 4.1 20.0 1.0 N C:ARG73 4.2 21.0 1.0 N C:GLU74 4.2 20.5 1.0 OE1 C:GLU74 4.3 21.3 1.0 C C:ASP72 4.4 21.2 1.0 CB C:ASP105 4.4 22.0 1.0 CG C:GLU22 4.7 15.7 1.0 CA C:GLU74 4.8 20.0 1.0 CG C:ASN106 4.9 23.7 1.0 O C:HOH2014 4.9 10.9 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