Calcium in PDB 5ulu: Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N

The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N, PDB code: 5ulu was solved by A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.34 / 2.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.238, 65.386, 114.651, 90.00, 98.62, 90.00
R / Rfree (%)	19.5 / 24.4

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N (pdb code 5ulu). 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 Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N, PDB code: 5ulu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2301 b:79.5 occ:1.00 O A:HOH2403 2.1 66.5 1.0 OE2 A:GLU2007 2.3 82.3 1.0 O A:HOH2404 2.4 85.0 1.0 OE2 A:GLU1947 2.5 72.2 1.0 OD1 A:ASP2005 2.6 95.9 1.0 OD2 A:ASP2041 2.7 81.1 1.0 OD1 A:ASP2041 2.9 81.0 1.0 CG A:ASP2041 3.1 81.4 1.0 CG A:ASP2005 3.3 93.3 1.0 CD A:GLU1947 3.4 75.2 1.0 CD A:GLU2007 3.4 85.2 1.0 OE1 A:GLU1947 3.7 69.2 1.0 OD2 A:ASP2005 3.8 0.5 1.0 CA A:CA2302 3.9 81.9 1.0 ND2 A:ASN2042 4.0 83.3 1.0 CG A:GLU2007 4.0 87.7 1.0 CB A:GLU2007 4.1 89.8 1.0 N A:GLU2007 4.3 90.3 1.0 CB A:ASP2005 4.3 89.9 1.0 CA A:ASP2005 4.4 90.5 1.0 CB A:ASP2041 4.4 83.2 1.0 N A:ARG2006 4.5 83.2 1.0 OE1 A:GLU2007 4.5 85.7 1.0 ND2 A:ASN1948 4.6 77.1 1.0 C A:ASP2005 4.7 88.9 1.0 CG A:GLU1947 4.8 78.3 1.0 OD1 A:ASN1948 4.8 79.8 1.0 CA A:GLU2007 4.9 88.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2302 b:81.9 occ:1.00 OE1 A:GLU1947 2.1 69.2 1.0 O A:ASP2039 2.3 88.7 1.0 OD1 A:ASP2038 2.3 76.9 1.0 OD1 A:ASP2074 2.3 83.2 1.0 OE2 A:GLU2007 2.4 82.3 1.0 OD1 A:ASP2041 2.6 81.0 1.0 OE1 A:GLU2007 2.6 85.7 1.0 CD A:GLU2007 2.8 85.2 1.0 CD A:GLU1947 3.2 75.2 1.0 C A:ASP2039 3.4 88.5 1.0 CG A:ASP2074 3.5 84.5 1.0 CG A:ASP2038 3.5 81.9 1.0 CG A:ASP2041 3.6 81.4 1.0 N A:ASP2039 3.6 85.6 1.0 OE2 A:GLU1947 3.7 72.2 1.0 CA A:CA2301 3.9 79.5 1.0 ND2 A:ASN2042 4.0 83.3 1.0 OD2 A:ASP2041 4.0 81.1 1.0 CA A:ASP2039 4.0 90.2 1.0 N A:ASP2041 4.1 81.5 1.0 CB A:ASP2074 4.2 87.9 1.0 CG A:GLU2007 4.2 87.7 1.0 OD2 A:ASP2038 4.2 82.8 1.0 CB A:ASP2039 4.3 95.2 1.0 OD2 A:ASP2074 4.4 82.3 1.0 NE A:ARG2006 4.5 0.3 1.0 C A:ASP2038 4.5 82.7 1.0 CG A:GLU1947 4.5 78.3 1.0 N A:ASN2040 4.5 90.3 1.0 CA A:ASP2074 4.5 89.2 1.0 CA A:ASP2038 4.5 82.9 1.0 CB A:ASP2038 4.6 83.8 1.0 CB A:ASP2041 4.8 83.2 1.0 CA A:ASN2040 4.8 88.8 1.0 NH2 A:ARG2006 4.8 0.7 1.0 CB A:ARG2006 4.8 84.6 1.0 CA A:ASP2041 4.9 81.4 1.0 O A:HOH2404 4.9 85.0 1.0 C A:ASN2040 5.0 87.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2303 b:83.4 occ:1.00 OD1 A:ASN2040 2.1 88.4 1.0 O A:ASN2042 2.2 81.5 1.0 OD2 A:ASP2074 2.2 82.3 1.0 OD1 A:ASP2072 2.4 82.3 1.0 OD2 A:ASP2072 2.4 84.9 1.0 O A:ASN2078 2.5 88.4 1.0 OD1 A:ASN2125 2.5 82.7 1.0 CG A:ASP2072 2.8 83.3 1.0 CG A:ASN2040 3.3 90.9 1.0 CG A:ASP2074 3.4 84.5 1.0 C A:ASN2042 3.4 80.1 1.0 CG A:ASN2125 3.4 84.8 1.0 C A:ASN2078 3.7 91.0 1.0 ND2 A:ASN2125 3.7 85.8 1.0 CB A:ASP2074 3.9 87.9 1.0 ND2 A:ASN2040 3.9 91.7 1.0 N A:ASN2042 4.0 75.4 1.0 CA A:ASN2042 4.1 81.2 1.0 CB A:ASN2042 4.3 87.5 1.0 CD A:PRO2044 4.3 76.6 1.0 CB A:ASP2072 4.4 84.0 1.0 OD1 A:ASP2074 4.4 83.2 1.0 N A:TRP2043 4.5 79.0 1.0 CD1 A:LEU2131 4.5 75.1 1.0 CB A:ASN2040 4.5 89.7 1.0 CA A:ASN2078 4.5 89.0 1.0 N A:GLY2079 4.6 95.3 1.0 CA A:ASN2040 4.6 88.8 1.0 CB A:ASN2125 4.6 84.8 1.0 CA A:GLY2079 4.6 95.0 1.0 CB A:ASN2078 4.7 87.0 1.0 CA A:TRP2043 4.8 77.2 1.0 C A:ASN2040 4.8 87.6 1.0 N A:ASP2074 4.8 86.3 1.0 N A:PRO2044 4.9 77.5 1.0 C A:TRP2043 4.9 78.2 1.0 N A:ASP2041 4.9 81.5 1.0 CA A:ASP2074 5.0 89.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2304 b:99.5 occ:1.00 OD1 A:ASP2110 2.0 0.2 1.0 OD2 A:ASP2146 2.2 95.4 1.0 OE2 A:GLU2112 2.4 91.3 1.0 OD1 A:ASP2146 2.5 94.7 1.0 OE2 A:GLU2057 2.5 95.0 1.0 CG A:ASP2146 2.7 93.7 1.0 CG A:ASP2110 3.1 0.5 1.0 O A:HOH2407 3.3 77.4 1.0 CD A:GLU2057 3.5 93.5 1.0 CD A:GLU2112 3.6 86.8 1.0 OD2 A:ASP2110 3.7 0.6 1.0 OE1 A:GLU2057 3.7 93.7 1.0 CA A:CA2305 3.9 91.0 1.0 OD1 A:ASN2058 4.0 98.6 1.0 CB A:ASP2146 4.2 94.0 1.0 CB A:ASP2110 4.2 0.1 1.0 OG A:SER2147 4.3 95.6 1.0 OE1 A:GLU2112 4.3 87.2 1.0 N A:ARG2111 4.4 92.7 1.0 CA A:ASP2110 4.4 99.2 1.0 CG A:GLU2112 4.5 87.2 1.0 N A:GLU2112 4.5 90.5 1.0 CB A:GLU2112 4.5 89.0 1.0 ND2 A:ASN2058 4.7 0.4 1.0 CG A:GLU2057 4.8 93.0 1.0 C A:ASP2110 4.8 97.0 1.0 CG A:ASN2058 4.8 0.6 1.0 C A:ASP2146 4.9 94.7 1.0 O A:ASP2146 4.9 99.4 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2305 b:91.0 occ:1.00 OE1 A:GLU2112 2.0 87.2 1.0 O A:ILE2144 2.1 89.8 1.0 OE1 A:GLU2057 2.2 93.7 1.0 OD1 A:ASP2179 2.3 93.4 1.0 OD1 A:ASP2143 2.4 91.4 1.0 OD1 A:ASP2146 2.6 94.7 1.0 CD A:GLU2112 2.7 86.8 1.0 OE2 A:GLU2112 2.7 91.3 1.0 CD A:GLU2057 3.3 93.5 1.0 C A:ILE2144 3.3 92.7 1.0 CG A:ASP2143 3.4 91.6 1.0 CG A:ASP2179 3.5 95.7 1.0 CG A:ASP2146 3.5 93.7 1.0 OE2 A:GLU2057 3.7 95.0 1.0 N A:ASP2146 3.9 91.0 1.0 N A:ILE2144 3.9 92.7 1.0 CA A:CA2304 3.9 99.5 1.0 OD2 A:ASP2143 3.9 87.5 1.0 OD2 A:ASP2146 4.1 95.4 1.0 CG A:GLU2112 4.1 87.2 1.0 CB A:ASP2179 4.1 90.9 1.0 CA A:ILE2144 4.2 93.2 1.0 N A:ASN2145 4.3 93.9 1.0 CA A:ASN2145 4.4 92.2 1.0 NE A:ARG2111 4.4 96.6 1.0 CB A:ASP2146 4.4 94.0 1.0 CA A:ASP2179 4.4 85.8 1.0 OD2 A:ASP2179 4.5 96.5 1.0 CB A:ARG2111 4.6 93.8 1.0 CB A:ASP2143 4.6 92.2 1.0 CG A:GLU2057 4.6 93.0 1.0 CA A:ASP2146 4.6 93.0 1.0 C A:ASN2145 4.7 97.4 1.0 CA A:ASP2143 4.7 91.1 1.0 C A:ASP2143 4.8 93.2 1.0 OG A:SER2147 4.8 95.6 1.0 CB A:ILE2144 4.8 94.8 1.0 N A:SER2147 4.9 94.5 1.0 NH2 A:ARG2111 5.0 94.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N


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 Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2306 b:91.6 occ:1.00 OD1 A:ASN2145 2.2 91.3 1.0 OD2 A:ASP2239 2.2 90.8 1.0 OD2 A:ASP2177 2.2 83.6 1.0 O A:SER2147 2.4 92.9 1.0 OD2 A:ASP2179 2.6 96.5 1.0 OD1 A:ASP2177 2.8 95.0 1.0 CG A:ASP2177 2.8 87.5 1.0 CG A:ASN2145 3.3 92.2 1.0 CG A:ASP2239 3.3 91.6 1.0 C A:SER2147 3.5 95.4 1.0 CB A:ASP2239 3.7 90.0 1.0 OG A:SER2242 3.7 95.0 1.0 ND2 A:ASN2145 3.7 94.5 1.0 CG A:ASP2179 3.7 95.7 1.0 N A:SER2147 3.8 94.5 1.0 CA A:SER2147 4.1 94.1 1.0 CB A:ASP2177 4.3 86.7 1.0 CB A:SER2242 4.3 96.3 1.0 CB A:ASP2179 4.4 90.9 1.0 OD1 A:ASP2239 4.4 89.4 1.0 C A:ASN2145 4.4 97.4 1.0 CB A:SER2147 4.4 90.9 1.0 N A:ARG2148 4.5 98.7 1.0 CB A:ASN2145 4.5 91.9 1.0 N A:ASP2146 4.6 91.0 1.0 O A:ASN2145 4.6 99.7 1.0 CD A:PRO2149 4.6 89.0 1.0 O A:HIS2247 4.7 97.5 1.0 CA A:ASN2145 4.7 92.2 1.0 OD1 A:ASP2179 4.7 93.4 1.0 CA A:SER2242 4.8 98.2 1.0 C A:ASP2146 4.9 94.7 1.0 N A:PRO2149 4.9 88.1 1.0 CA A:ARG2148 5.0 96.7 1.0

A.Jaiganesh, P.De-La-Torre, A.A.Patel, D.J.Termine, F.Velez-Cortes, C.Chen, M.Sotomayor. Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Structure V. 26 1210 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003