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

Protein crystallography data

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

Other elements in 2wd0:

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

Sodium Binding Sites:

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 2wd0

Go back to Sodium Binding Sites List in 2wd0
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 2wd0

Go back to Sodium Binding Sites List in 2wd0
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

Reference:

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
Page generated: Tue Dec 15 05:57:17 2020

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