Calcium in PDB 5un2: Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W

The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W, PDB code: 5un2 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)	50.00 / 2.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	189.475, 73.908, 49.375, 90.00, 96.62, 90.00
R / Rfree (%)	19.6 / 23.6

The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W (pdb code 5un2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W, PDB code: 5un2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2301 b:58.3 occ:1.00 OE2 A:GLU1947 2.4 67.6 1.0 OE1 A:GLU2007 2.4 75.5 1.0 OD2 A:ASP2041 2.5 67.9 1.0 OD1 A:ASP2005 2.9 68.8 1.0 CG A:ASP2041 3.4 66.2 1.0 CD A:GLU1947 3.4 67.9 1.0 OD1 A:ASP2041 3.5 65.1 1.0 CG A:ASP2005 3.5 69.5 1.0 CD A:GLU2007 3.7 75.0 1.0 OE1 A:GLU1947 3.9 68.8 1.0 OD2 A:ASP2005 4.0 71.5 1.0 OD1 A:ASN1948 4.1 69.3 1.0 CA A:ASP2005 4.2 67.0 1.0 N A:TRP2006 4.2 65.2 1.0 OE2 A:GLU2007 4.3 74.4 1.0 CB A:ASP2005 4.4 68.2 1.0 ND2 A:ASN2042 4.5 66.1 1.0 CA A:CA2302 4.5 66.8 1.0 N A:GLU2007 4.5 69.3 1.0 ND2 A:ASN1948 4.5 70.9 1.0 C A:ASP2005 4.5 65.8 1.0 CG A:GLU1947 4.7 67.1 1.0 CG A:GLU2007 4.7 75.7 1.0 CB A:GLU2007 4.7 74.7 1.0 CG A:ASN1948 4.7 70.5 1.0 CB A:ASP2041 4.7 66.2 1.0 O A:ILE2004 5.0 70.4 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2302 b:66.8 occ:1.00 OE2 A:GLU2007 2.3 74.4 1.0 OD1 A:ASP2038 2.3 66.9 1.0 OD1 A:ASP2041 2.4 65.1 1.0 O A:ASP2039 2.4 70.2 1.0 OE1 A:GLU1947 2.4 68.8 1.0 OD1 A:ASP2074 2.4 63.6 1.0 CD A:GLU2007 3.1 75.0 1.0 OE1 A:GLU2007 3.3 75.5 1.0 CG A:ASP2041 3.4 66.2 1.0 CD A:GLU1947 3.5 67.9 1.0 C A:ASP2039 3.5 71.6 1.0 CG A:ASP2038 3.5 67.4 1.0 CG A:ASP2074 3.6 62.7 1.0 N A:ASP2039 3.8 66.5 1.0 OD2 A:ASP2041 4.0 67.9 1.0 OE2 A:GLU1947 4.0 67.6 1.0 ND2 A:ASN2042 4.0 66.1 1.0 N A:ASP2041 4.0 62.8 1.0 OD2 A:ASP2038 4.2 69.5 1.0 CA A:ASP2039 4.2 69.7 1.0 CB A:ASP2074 4.4 62.8 1.0 CA A:ASP2074 4.4 64.1 1.0 CA A:CA2301 4.5 58.3 1.0 OD2 A:ASP2074 4.5 61.9 1.0 CG A:GLU2007 4.5 75.7 1.0 CB A:ASP2041 4.5 66.2 1.0 CB A:TRP2006 4.5 64.5 1.0 N A:ASN2040 4.6 75.0 1.0 C A:ASP2038 4.6 66.1 1.0 CB A:ASP2038 4.7 65.5 1.0 CA A:ASP2038 4.7 64.1 1.0 CA A:ASP2041 4.7 64.3 1.0 CG A:GLU1947 4.8 67.1 1.0 CA A:ASN2040 4.8 77.6 1.0 C A:ASN2040 4.9 78.6 1.0 CE3 A:TRP2006 4.9 66.5 1.0 C A:ASP2041 5.0 64.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2303 b:49.6 occ:1.00 OD1 A:ASN2040 2.4 82.0 1.0 O A:ASN2042 2.5 61.9 1.0 OD2 A:ASP2074 2.5 61.9 1.0 O A:ASN2078 2.5 59.8 1.0 OD2 A:ASP2072 2.8 61.7 1.0 OD2 A:ASP2125 2.8 61.1 1.0 OD1 A:ASP2072 3.1 63.5 1.0 CG A:ASP2125 3.3 61.3 1.0 CG A:ASP2072 3.4 62.5 1.0 CG A:ASP2074 3.5 62.7 1.0 CG A:ASN2040 3.6 83.8 1.0 CB A:ASP2125 3.6 60.7 1.0 C A:ASN2042 3.7 63.1 1.0 C A:ASN2078 3.7 60.8 1.0 CB A:ASP2074 3.9 62.8 1.0 OD1 A:ASP2125 4.1 62.3 1.0 N A:ASN2042 4.2 63.5 1.0 ND2 A:ASN2040 4.2 88.0 1.0 CA A:ASN2042 4.4 63.9 1.0 CA A:ASN2078 4.4 61.7 1.0 CD A:PRO2044 4.5 60.1 1.0 CB A:ASN2078 4.5 62.4 1.0 OD1 A:ASP2074 4.6 63.6 1.0 CB A:ASN2042 4.7 63.9 1.0 N A:TRP2043 4.7 64.4 1.0 N A:GLY2079 4.7 61.6 1.0 CD1 A:LEU2131 4.7 66.8 1.0 CB A:ASN2040 4.8 81.5 1.0 CA A:ASN2040 4.8 77.6 1.0 CB A:ASP2072 4.9 62.7 1.0 CG A:PRO2044 4.9 58.8 1.0 C A:ASN2040 4.9 78.6 1.0 CA A:TRP2043 4.9 63.5 1.0 CB A:LEU2131 4.9 64.6 1.0 N A:PRO2044 4.9 60.5 1.0 N A:ASP2041 5.0 62.8 1.0 CA A:GLY2079 5.0 61.4 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2304 b:31.1 occ:1.00 OD1 A:ASP2110 2.3 45.4 1.0 OE2 A:GLU2057 2.4 46.4 1.0 OE1 A:GLU2112 2.5 42.1 1.0 OD2 A:ASP2146 2.7 45.7 1.0 OD1 A:ASP2146 2.7 42.6 1.0 CG A:ASP2146 3.0 44.5 1.0 CG A:ASP2110 3.3 46.0 1.0 CD A:GLU2057 3.5 46.6 1.0 CD A:GLU2112 3.7 42.5 1.0 OD2 A:ASP2110 3.9 45.6 1.0 CA A:CA2305 3.9 32.8 1.0 OE1 A:GLU2057 4.0 46.8 1.0 CB A:ASP2110 4.3 46.8 1.0 OD1 A:ASN2058 4.4 46.6 1.0 CA A:ASP2110 4.4 46.8 1.0 N A:ARG2111 4.4 45.4 1.0 CB A:ASP2146 4.5 45.2 1.0 CG A:GLU2112 4.5 42.3 1.0 CB A:GLU2112 4.6 42.3 1.0 N A:GLU2112 4.6 44.0 1.0 OE2 A:GLU2112 4.6 43.0 1.0 CG A:GLU2057 4.7 47.6 1.0 C A:ASP2110 4.8 46.0 1.0 O A:ASP2146 4.8 41.6 1.0 C A:ASP2146 5.0 41.3 1.0 CB A:SER2147 5.0 38.3 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2305 b:32.8 occ:1.00 O A:ILE2144 2.2 39.2 1.0 OD1 A:ASP2179 2.3 41.9 1.0 OE1 A:GLU2057 2.4 46.8 1.0 OE2 A:GLU2112 2.4 43.0 1.0 OE1 A:GLU2112 2.5 42.1 1.0 OD1 A:ASP2146 2.6 42.6 1.0 OD1 A:ASP2143 2.6 40.6 1.0 CD A:GLU2112 2.8 42.5 1.0 CD A:GLU2057 3.3 46.6 1.0 C A:ILE2144 3.4 40.9 1.0 CG A:ASP2146 3.5 44.5 1.0 CG A:ASP2179 3.5 41.7 1.0 OE2 A:GLU2057 3.6 46.4 1.0 CG A:ASP2143 3.7 42.4 1.0 N A:ASP2146 3.8 43.3 1.0 CA A:CA2304 3.9 31.1 1.0 N A:ILE2144 4.0 42.1 1.0 OD2 A:ASP2146 4.1 45.7 1.0 CB A:ASP2179 4.1 43.4 1.0 CG A:GLU2112 4.3 42.3 1.0 OD2 A:ASP2143 4.3 43.5 1.0 N A:ASN2145 4.3 41.4 1.0 CA A:ASN2145 4.3 39.9 1.0 CA A:ILE2144 4.4 42.6 1.0 CA A:ASP2179 4.4 43.6 1.0 OD2 A:ASP2179 4.4 40.2 1.0 CB A:ASP2146 4.5 45.2 1.0 NE A:ARG2111 4.5 48.8 1.0 CA A:ASP2146 4.6 43.4 1.0 C A:ASN2145 4.6 39.0 1.0 CG A:GLU2057 4.6 47.6 1.0 CA A:ASP2143 4.7 43.0 1.0 CB A:ARG2111 4.7 46.1 1.0 CB A:ASP2143 4.8 43.5 1.0 N A:SER2147 4.9 40.1 1.0 C A:ASP2143 4.9 43.6 1.0 CB A:SER2147 4.9 38.3 1.0 C A:ASP2146 4.9 41.3 1.0 CB A:ILE2144 5.0 43.0 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


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 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2306 b:37.2 occ:1.00 O A:SER2147 2.4 36.7 1.0 OD1 A:ASN2145 2.4 38.4 1.0 OD2 A:ASP2177 2.4 41.0 1.0 OD2 A:ASP2179 2.5 40.2 1.0 OD1 A:ASP2177 2.7 42.0 1.0 OD2 A:ASP2239 2.7 42.7 1.0 CG A:ASP2177 2.9 41.0 1.0 C A:SER2147 3.4 37.5 1.0 CG A:ASP2239 3.6 43.1 1.0 CG A:ASN2145 3.6 40.0 1.0 CB A:ASP2239 3.6 41.5 1.0 CG A:ASP2179 3.7 41.7 1.0 N A:SER2147 3.7 40.1 1.0 CB A:SER2242 3.8 45.7 1.0 O A:HIS2247 3.9 39.8 1.0 CA A:SER2147 4.1 38.7 1.0 N A:ARG2148 4.3 37.7 1.0 ND2 A:ASN2145 4.3 41.1 1.0 CB A:ASP2179 4.3 43.4 1.0 C A:ASN2145 4.4 39.0 1.0 CA A:ARG2148 4.4 37.1 1.0 N A:ASP2146 4.4 43.3 1.0 CB A:ASP2177 4.5 39.6 1.0 O A:ASN2145 4.5 40.1 1.0 CA A:SER2242 4.6 48.2 1.0 OD1 A:ASP2179 4.6 41.9 1.0 CD A:PRO2149 4.7 35.9 1.0 C A:ASP2146 4.7 41.3 1.0 OD1 A:ASP2239 4.7 44.8 1.0 C A:ARG2148 4.7 35.7 1.0 CB A:SER2147 4.8 38.3 1.0 CB A:ASN2145 4.8 41.3 1.0 N A:PRO2149 4.8 35.2 1.0 CA A:ASN2145 4.8 39.9 1.0 OG A:SER2242 5.0 47.1 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2307 b:34.3 occ:1.00 OD1 A:ASP2262 2.4 35.5 1.0 OE1 A:GLU2162 2.4 33.3 1.0 O A:VAL2263 2.4 43.3 1.0 OE1 A:GLU2226 2.8 35.5 1.0 OE2 A:GLU2226 2.8 34.3 1.0 CD A:GLU2226 3.0 35.1 1.0 CD A:GLU2162 3.5 32.1 1.0 CG A:ASP2262 3.5 37.2 1.0 C A:VAL2263 3.6 43.9 1.0 N A:VAL2263 3.7 37.9 1.0 OE2 A:GLU2162 3.9 31.2 1.0 OD2 A:ASP2262 4.0 39.3 1.0 CA A:VAL2263 4.2 41.1 1.0 CG A:GLU2226 4.3 36.1 1.0 CA A:CA2308 4.3 38.3 1.0 N A:ASN2264 4.6 48.5 1.0 CB A:ASN2264 4.7 52.0 1.0 C A:ASP2262 4.7 37.0 1.0 CB A:ASP2262 4.7 37.0 1.0 CA A:ASP2262 4.8 35.4 1.0 CG A:GLU2162 4.8 31.5 1.0 O A:HOH2405 4.8 17.5 1.0 CB A:VAL2263 4.8 40.1 1.0 CA A:ASN2264 4.9 51.4 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Mouse Cadherin-23 EC19-21 with Non-Syndromic Deafness (DFNB12) Associated Mutation R2029W within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2308 b:38.3 occ:1.00 OD1 A:ASN2224 2.2 36.3 1.0 OE2 A:GLU2162 2.4 31.2 1.0 OE2 A:GLU2226 2.7 34.3 1.0 CG A:ASN2224 3.1 36.1 1.0 CD A:GLU2162 3.4 32.1 1.0 O A:HOH2438 3.8 20.8 1.0 CD A:GLU2226 3.9 35.1 1.0 OE1 A:GLU2162 3.9 33.3 1.0 ND2 A:ASN2224 3.9 37.9 1.0 CB A:ASN2224 4.0 35.1 1.0 CA A:ASN2224 4.0 34.0 1.0 N A:ARG2225 4.3 34.3 1.0 CA A:CA2307 4.3 34.3 1.0 C A:ASN2224 4.6 34.1 1.0 CG A:GLU2162 4.6 31.5 1.0 N A:GLU2226 4.7 33.7 1.0 CG A:GLU2226 4.7 36.1 1.0 OE1 A:GLU2226 4.8 35.5 1.0 CB A:GLU2226 4.8 35.5 1.0 O A:LEU2223 5.0 34.3 1.0 CB A:GLU2162 5.0 29.8 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