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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Nonsyndromic Deafness (DFNB12) Associated Mutant D124G of Mouse Cadherin-23 EC1-2, PDB code: 2wd0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca501

b:22.9
occ:1.00
 OD1 A:ASN104 2.2 22.3 1.0
O A:GLY142 2.2 23.4 1.0
O A:ASN106 2.3 21.7 1.0
OD2 A:ASP138 2.4 23.8 1.0
OD1 A:ASP136 2.4 24.1 1.0
OD2 A:ASP187 2.6 31.6 1.0
OD2 A:ASP136 2.6 22.9 1.0
CG A:ASP136 2.8 24.4 1.0
CG A:ASP187 3.3 32.1 1.0
CG A:ASP138 3.3 22.8 1.0
CG A:ASN104 3.4 21.4 1.0
C A:ASN106 3.4 22.0 1.0
C A:GLY142 3.4 23.8 1.0
CB A:ASP138 3.6 22.9 1.0
CB A:ASP187 3.7 32.4 1.0
ND2 A:ASN104 4.0 21.5 1.0
N A:ASN106 4.0 21.8 1.0
CA A:ASN106 4.1 22.0 1.0
CA A:GLY142 4.2 23.8 1.0
OD1 A:ASP187 4.2 32.7 1.0
CB A:ASN106 4.2 22.1 1.0
CB A:ASP136 4.3 24.8 1.0
N A:GLY143 4.4 24.0 1.0
OD1 A:ASP138 4.5 22.8 1.0
N A:ALA107 4.5 22.4 1.0
CB A:ASN104 4.6 20.7 1.0
CA A:GLY143 4.6 24.7 1.0
CA A:ASN104 4.8 20.5 1.0
CD1 A:LEU194 4.8 30.3 1.0
CA A:ALA107 4.8 22.8 1.0
N A:ASP138 4.8 22.7 1.0
CA A:ASP138 4.9 22.9 1.0
C A:ASN104 5.0 20.4 1.0
CB A:LEU194 5.0 32.1 1.0
N A:ASP105 5.0 20.6 1.0

Calcium binding site 2 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca502

b:19.8
occ:1.00
 OD1 A:ASP105 2.2 18.7 1.0
OE1 A:GLU74 2.2 21.2 1.0
O A:VAL103 2.3 20.0 1.0
OE1 A:GLU22 2.3 21.5 1.0
OD1 A:ASP138 2.4 22.8 1.0
CL A:CL701 2.6 33.6 1.0
OE2 A:GLU74 2.7 22.1 1.0
CD A:GLU74 2.8 22.1 1.0
CG A:ASP105 3.3 20.8 1.0
CD A:GLU22 3.4 21.0 1.0
CG A:ASP138 3.4 22.8 1.0
C A:VAL103 3.5 20.2 1.0
N A:VAL103 3.7 19.8 1.0
OE2 A:GLU22 3.7 21.2 1.0
NH1 A:ARG73 3.9 27.7 1.0
OD2 A:ASP105 3.9 22.4 1.0
N A:ASP105 4.0 20.6 1.0
OD1 A:ASN106 4.0 22.3 1.0
CB A:ASP138 4.1 22.9 1.0
CA A:ASP138 4.2 22.9 1.0
CG A:GLU74 4.2 22.0 1.0
CA A:VAL103 4.2 19.8 1.0
NA A:NA601 4.2 29.0 1.0
OD2 A:ASP138 4.4 23.8 1.0
N A:ASN104 4.4 20.4 1.0
CB A:ASP105 4.5 20.5 1.0
CA A:ASN104 4.6 20.5 1.0
CG A:GLU22 4.6 20.6 1.0
C A:GLY102 4.7 19.8 1.0
CA A:GLY102 4.7 19.8 1.0
CA A:ASP105 4.7 20.7 1.0
C A:ASN104 4.8 20.4 1.0
CB A:ARG73 4.9 22.7 1.0

Calcium binding site 3 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca binding site number 3 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:Ca504

b:14.2
occ:1.00
 OD2 A:ASP41 2.1 18.4 1.0
O A:ARG5 2.2 18.3 1.0
OD1 A:ASN4 2.3 21.7 1.0
OD2 A:ASP87 2.4 34.0 1.0
OD1 A:ASP39 2.5 23.5 1.0
OD1 A:ASP37 2.6 25.8 1.0
OD2 A:ASP37 2.8 26.0 1.0
CG A:ASP37 3.0 24.8 1.0
CG A:ASP41 3.3 20.8 1.0
CG A:ASN4 3.3 20.1 1.0
CG A:ASP87 3.4 31.6 1.0
C A:ARG5 3.4 18.6 1.0
CG A:ASP39 3.5 23.6 1.0
CB A:ASP87 3.6 30.2 1.0
ND2 A:ASN4 3.8 17.8 1.0
CB A:ASP39 3.8 23.1 1.0
CB A:ASP41 4.0 21.0 1.0
N A:ARG5 4.0 19.4 1.0
CA A:LEU6 4.3 18.2 1.0
N A:LEU6 4.3 18.5 1.0
CA A:ARG5 4.3 19.0 1.0
OD1 A:ASP41 4.3 21.7 1.0
CD A:PRO7 4.4 17.9 1.0
N A:PRO7 4.5 17.9 1.0
CB A:ASP37 4.5 24.6 1.0
OD1 A:ASP87 4.5 32.9 1.0
C A:LEU6 4.5 18.0 1.0
CB A:ASN4 4.6 20.5 1.0
OD2 A:ASP39 4.7 23.0 1.0
OE1 A:GLN89 4.7 43.8 1.0
N A:ASP39 4.8 23.0 1.0
C A:ASN4 4.8 20.0 1.0
CA A:ASP39 4.9 22.7 1.0
CA A:ASN4 4.9 20.5 1.0
CB A:ARG5 5.0 19.0 1.0

Calcium binding site 4 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca binding site number 4 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:Ca501

b:26.4
occ:1.00
 OD1 C:ASP105 2.2 22.1 1.0
O C:VAL103 2.3 21.2 1.0
OE1 C:GLU74 2.3 21.3 1.0
OE1 C:GLU22 2.4 15.3 1.0
OD1 C:ASP138 2.5 28.1 1.0
OE2 C:GLU74 2.6 21.7 1.0
CL C:CL701 2.7 41.8 1.0
CD C:GLU74 2.8 21.7 1.0
CG C:ASP105 3.3 22.5 1.0
CD C:GLU22 3.4 15.4 1.0
C C:VAL103 3.5 21.0 1.0
CG C:ASP138 3.5 27.4 1.0
OE2 C:GLU22 3.7 13.0 1.0
N C:VAL103 3.8 20.5 1.0
OD2 C:ASP105 3.8 24.8 1.0
NH1 C:ARG73 3.8 28.3 1.0
NA C:NA601 4.0 26.3 1.0
N C:ASP105 4.0 21.6 1.0
CB C:ASP138 4.1 26.9 1.0
OD1 C:ASN106 4.1 26.4 1.0
CA C:ASP138 4.2 26.7 1.0
CA C:VAL103 4.2 20.6 1.0
CG C:GLU74 4.3 20.8 1.0
OD2 C:ASP138 4.5 27.6 1.0
CB C:ASP105 4.5 22.0 1.0
N C:ASN104 4.5 21.2 1.0
CA C:ASN104 4.7 21.4 1.0
CG C:GLU22 4.7 15.7 1.0
C C:GLY102 4.7 20.3 1.0
CA C:GLY102 4.8 20.4 1.0
CA C:ASP105 4.8 22.0 1.0
O C:HOH2016 4.8 31.3 1.0
C C:ASN104 4.8 21.4 1.0
CB C:ARG73 4.8 21.4 1.0
CB C:VAL103 5.0 20.6 1.0

Calcium binding site 5 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca503

b:21.9
occ:1.00
 O C:ASN106 2.2 22.4 1.0
OD1 C:ASN104 2.3 20.6 1.0
O C:GLY142 2.3 25.9 1.0
OD2 C:ASP138 2.3 27.6 1.0
OD2 C:ASP187 2.5 33.8 1.0
OD2 C:ASP136 2.5 27.7 1.0
OD1 C:ASP136 2.6 27.2 1.0
CG C:ASP136 2.9 28.0 1.0
CG C:ASP187 3.3 35.5 1.0
C C:ASN106 3.4 22.9 1.0
CG C:ASP138 3.4 27.4 1.0
CG C:ASN104 3.5 21.7 1.0
C C:GLY142 3.5 26.1 1.0
CB C:ASP187 3.7 36.3 1.0
CB C:ASP138 3.8 26.9 1.0
N C:ASN106 4.1 22.7 1.0
ND2 C:ASN104 4.1 21.9 1.0
CA C:ASN106 4.1 23.0 1.0
CA C:GLY142 4.2 26.1 1.0
OD1 C:ASP187 4.3 34.8 1.0
CB C:ASN106 4.4 23.0 1.0
CB C:ASP136 4.4 28.2 1.0
N C:ALA107 4.4 23.1 1.0
OD1 C:ASP138 4.5 28.1 1.0
N C:GLY143 4.5 26.3 1.0
CD1 C:LEU194 4.6 32.8 1.0
CA C:ALA107 4.7 23.2 1.0
CB C:ASN104 4.7 21.6 1.0
CA C:GLY143 4.8 26.6 1.0
CA C:ASN104 4.8 21.4 1.0
CB C:LEU194 4.8 35.0 1.0
C C:ALA107 4.9 23.2 1.0
N C:ASP105 4.9 21.6 1.0

Calcium binding site 6 out of 6 in 2wd0

Go back to Calcium Binding Sites List in 2wd0
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca504

b:30.4
occ:1.00
 OD2 C:ASP41 2.3 22.0 1.0
OD1 C:ASP37 2.5 29.3 1.0
OD1 C:ASN4 2.5 32.5 1.0
O C:ARG5 2.5 31.9 1.0
OD2 C:ASP39 2.6 25.1 1.0
OD2 C:ASP87 2.6 34.8 1.0
OD2 C:ASP37 2.9 26.9 1.0
CG C:ASP37 3.0 27.7 1.0
CG C:ASP87 3.5 36.2 1.0
C C:ARG5 3.5 31.8 1.0
CG C:ASP39 3.5 25.2 1.0
CG C:ASP41 3.5 21.7 1.0
CB C:ASP87 3.6 35.3 1.0
CG C:ASN4 3.7 34.1 1.0
CB C:ASP39 4.0 25.0 1.0
CA C:LEU6 4.1 29.7 1.0
N C:LEU6 4.2 30.6 1.0
CB C:ASP41 4.2 21.8 1.0
ND2 C:ASN4 4.3 33.4 1.0
N C:ARG5 4.3 33.2 1.0
C C:LEU6 4.5 28.9 1.0
OD1 C:ASP41 4.5 21.4 1.0
CA C:ARG5 4.5 32.6 1.0
OD1 C:ASP39 4.5 26.1 1.0
CB C:ASP37 4.5 26.7 1.0
N C:PRO7 4.6 28.0 1.0
CD C:PRO7 4.6 27.9 1.0
OD1 C:ASP87 4.7 35.9 1.0
C C:ASN4 4.8 34.0 1.0
CB C:ASN4 4.9 34.6 1.0
CA C:ASN4 5.0 34.6 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 Jul 8 09:02:49 2025

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