Calcium in PDB 5i8d: Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P

The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P, PDB code: 5i8d 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)	111.36 / 2.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.722, 67.754, 112.782, 90.00, 99.12, 90.00
R / Rfree (%)	21.9 / 25.3

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P (pdb code 5i8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P, PDB code: 5i8d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2301 b:71.8 occ:1.00 OD1 A:ASN1930 2.2 76.0 1.0 OD2 A:ASP1968 2.4 76.1 1.0 OD2 A:ASP2022 2.4 74.0 1.0 O A:ASN1932 2.4 81.7 1.0 O A:TYR1972 2.5 75.5 1.0 OD2 A:ASP1966 2.6 61.0 1.0 OD1 A:ASP1966 2.7 60.4 1.0 CG A:ASP1966 3.0 61.3 1.0 CG A:ASN1930 3.4 79.7 1.0 CG A:ASP2022 3.5 74.0 1.0 C A:ASN1932 3.5 79.6 1.0 CG A:ASP1968 3.6 77.6 1.0 C A:TYR1972 3.7 78.7 1.0 CB A:ASP2022 3.8 72.6 1.0 ND2 A:ASN1930 3.9 80.0 1.0 CB A:ASP1968 4.1 77.7 1.0 CB A:TYR1972 4.2 83.4 1.0 CA A:HIS1933 4.2 75.2 1.0 N A:HIS1933 4.2 77.7 1.0 CA A:TYR1972 4.4 82.0 1.0 N A:ASN1932 4.5 81.7 1.0 CA A:ASN1932 4.5 80.5 1.0 CB A:ASP1966 4.5 62.4 1.0 OD1 A:ASP2022 4.6 74.1 1.0 OD1 A:ASP1968 4.6 78.2 1.0 CB A:ASN1930 4.6 83.5 1.0 CA A:ASN1930 4.7 84.4 1.0 CB A:ASN1932 4.8 78.7 1.0 N A:ALA1973 4.8 78.5 1.0 C A:HIS1933 4.9 72.0 1.0 CD1 A:LEU2026 5.0 79.0 1.0 C A:ASN1930 5.0 84.9 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2302 b:66.1 occ:1.00 O A:HOH2404 2.2 53.4 1.0 OD2 A:ASP2041 2.3 75.1 1.0 OD1 A:ASP2005 2.3 85.2 1.0 OE2 A:GLU1947 2.5 79.8 1.0 OE1 A:GLU2007 2.5 79.9 1.0 CG A:ASP2041 3.1 73.0 1.0 OD1 A:ASP2041 3.3 73.3 1.0 CD A:GLU1947 3.3 79.7 1.0 CG A:ASP2005 3.4 85.0 1.0 OE1 A:GLU1947 3.7 78.3 1.0 CD A:GLU2007 3.8 81.0 1.0 CB A:ASP2005 3.9 84.3 1.0 CA A:ASP2005 4.0 82.9 1.0 OD1 A:ASN1948 4.0 77.7 1.0 N A:ARG2006 4.1 79.5 1.0 CA A:CA2303 4.2 69.6 1.0 C A:ASP2005 4.3 81.8 1.0 ND2 A:ASN1948 4.4 79.5 1.0 OD2 A:ASP2005 4.4 86.5 1.0 ND2 A:ASN2042 4.5 74.4 1.0 N A:GLU2007 4.5 80.0 1.0 CG A:GLU1947 4.5 79.5 1.0 CB A:ASP2041 4.6 71.6 1.0 CB A:GLU2007 4.6 81.5 1.0 CG A:ASN1948 4.6 79.4 1.0 CG A:GLU2007 4.6 82.0 1.0 OE2 A:GLU2007 4.6 81.6 1.0 CB A:GLU1947 5.0 78.5 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2303 b:69.6 occ:1.00 OE1 A:GLU1947 2.3 78.3 1.0 OD1 A:ASP2041 2.4 73.3 1.0 OD1 A:ASP2074 2.5 75.3 1.0 OD1 A:ASP2038 2.5 85.0 1.0 O A:ASP2039 2.5 78.4 1.0 OE2 A:GLU2007 2.6 81.6 1.0 OE1 A:GLU2007 2.7 79.9 1.0 CD A:GLU2007 3.0 81.0 1.0 CD A:GLU1947 3.4 79.7 1.0 CG A:ASP2074 3.5 76.6 1.0 CG A:ASP2041 3.6 73.0 1.0 CG A:ASP2038 3.7 86.6 1.0 OE2 A:GLU1947 3.7 79.8 1.0 C A:ASP2039 3.7 80.3 1.0 ND2 A:ASN2042 3.9 74.4 1.0 N A:ASP2039 4.0 81.2 1.0 N A:ASP2041 4.1 69.5 1.0 CA A:CA2302 4.2 66.1 1.0 CB A:ASP2074 4.2 77.8 1.0 OD2 A:ASP2038 4.2 89.1 1.0 OD2 A:ASP2041 4.2 75.1 1.0 NE A:ARG2006 4.2 91.8 1.0 OD2 A:ASP2074 4.3 75.2 1.0 CG A:GLU2007 4.4 82.0 1.0 CA A:ASP2039 4.4 81.2 1.0 CA A:ASP2074 4.4 79.3 1.0 CB A:ASP2041 4.7 71.6 1.0 CG A:GLU1947 4.7 79.5 1.0 N A:ASN2040 4.7 81.8 1.0 CB A:ARG2006 4.8 82.0 1.0 CA A:ASP2041 4.8 70.0 1.0 CB A:ASP2038 4.9 85.1 1.0 O A:HOH2404 4.9 53.4 1.0 NH1 A:ARG2006 4.9 97.4 1.0 CB A:ASP2039 4.9 80.9 1.0 CA A:ASP2038 4.9 82.1 1.0 CA A:ASN2040 4.9 82.4 1.0 C A:ASP2038 4.9 82.3 1.0 CD A:ARG2006 5.0 88.0 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2304 b:72.8 occ:1.00 O A:ASN2042 2.3 68.4 1.0 OD1 A:ASN2040 2.3 84.3 1.0 OD2 A:ASP2125 2.4 71.4 1.0 OD2 A:ASP2074 2.4 75.2 1.0 OD2 A:ASP2072 2.5 73.8 1.0 O A:ASN2078 2.5 75.2 1.0 OD1 A:ASP2072 2.9 75.5 1.0 CG A:ASP2072 3.1 75.3 1.0 CG A:ASP2125 3.4 73.9 1.0 CG A:ASP2074 3.5 76.6 1.0 CG A:ASN2040 3.5 85.6 1.0 C A:ASN2042 3.5 69.9 1.0 C A:ASN2078 3.7 76.2 1.0 CB A:ASP2074 3.8 77.8 1.0 CB A:ASP2125 4.0 75.5 1.0 ND2 A:ASN2040 4.1 87.9 1.0 CD A:PRO2044 4.2 70.6 1.0 N A:ASN2042 4.2 69.9 1.0 CA A:ASN2042 4.3 70.8 1.0 OD1 A:ASP2125 4.4 74.3 1.0 CA A:ASN2078 4.5 76.5 1.0 CB A:ASN2042 4.5 71.8 1.0 N A:TRP2043 4.5 71.0 1.0 OD1 A:ASP2074 4.6 75.3 1.0 CB A:ASN2078 4.6 76.4 1.0 CB A:ASP2072 4.6 75.7 1.0 CD1 A:LEU2131 4.6 69.7 1.0 CB A:ASN2040 4.7 84.5 1.0 N A:GLY2079 4.7 77.8 1.0 CA A:ASN2040 4.7 82.4 1.0 CA A:TRP2043 4.7 71.6 1.0 N A:PRO2044 4.8 71.5 1.0 CB A:LEU2131 4.8 70.4 1.0 C A:ASN2040 4.8 82.0 1.0 C A:TRP2043 4.8 71.8 1.0 CA A:GLY2079 4.9 77.5 1.0 N A:ASP2041 5.0 69.5 1.0 N A:ASP2074 5.0 79.1 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2305 b:77.1 occ:1.00 OE1 A:GLU2057 1.9 66.2 1.0 OD1 A:ASP2110 2.3 68.8 1.0 OE2 A:GLU2112 2.5 64.4 1.0 OD1 A:ASP2146 2.6 93.0 1.0 OD2 A:ASP2146 2.7 99.6 1.0 CG A:ASP2146 3.0 95.7 1.0 CD A:GLU2057 3.1 66.7 1.0 CG A:ASP2110 3.3 69.3 1.0 CD A:GLU2112 3.7 65.2 1.0 CA A:CA2306 3.8 63.6 1.0 OD2 A:ASP2110 3.9 68.8 1.0 OE2 A:GLU2057 3.9 63.6 1.0 CG A:GLU2057 4.1 67.7 1.0 CG A:GLU2112 4.3 65.7 1.0 CB A:GLU2112 4.3 66.8 1.0 CB A:ASP2110 4.4 70.2 1.0 CB A:ASP2146 4.5 95.5 1.0 N A:GLU2112 4.5 66.6 1.0 CA A:ASP2110 4.6 69.5 1.0 OE1 A:GLU2112 4.7 63.7 1.0 ND2 A:ASN2058 4.7 72.5 1.0 N A:ARG2111 4.7 67.5 1.0 OD1 A:ASN2058 4.8 73.6 1.0 C A:ASP2146 4.8 87.2 1.0 O A:ASP2146 4.9 88.8 1.0 CB A:SER2147 4.9 80.6 1.0 C A:ASP2110 4.9 68.9 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2306 b:63.6 occ:1.00 O A:ILE2144 2.3 65.2 1.0 OD1 A:ASP2143 2.3 62.0 1.0 OE2 A:GLU2112 2.4 64.4 1.0 OD1 A:ASP2179 2.4 81.6 1.0 OE2 A:GLU2057 2.6 63.6 1.0 OD1 A:ASP2146 2.7 93.0 1.0 OE1 A:GLU2112 2.7 63.7 1.0 CD A:GLU2112 2.9 65.2 1.0 OE1 A:GLU2057 3.3 66.2 1.0 CD A:GLU2057 3.3 66.7 1.0 CG A:ASP2143 3.5 63.1 1.0 C A:ILE2144 3.5 66.6 1.0 CG A:ASP2179 3.6 79.1 1.0 CG A:ASP2146 3.7 95.7 1.0 CA A:CA2305 3.8 77.1 1.0 N A:ILE2144 4.0 66.9 1.0 N A:ASP2146 4.0 89.7 1.0 OD2 A:ASP2143 4.1 63.2 1.0 CG A:GLU2112 4.3 65.7 1.0 NE A:ARG2111 4.3 71.3 1.0 OD2 A:ASP2146 4.4 99.6 1.0 N A:ASN2145 4.4 66.5 1.0 CA A:ILE2144 4.4 68.4 1.0 CA A:ASN2145 4.4 64.5 1.0 OD2 A:ASP2179 4.5 77.2 1.0 CB A:ASP2143 4.5 65.0 1.0 CB A:ASP2179 4.5 78.0 1.0 CA A:ASP2143 4.5 65.3 1.0 CB A:ARG2111 4.6 68.2 1.0 CA A:ASP2179 4.7 77.8 1.0 C A:ASP2143 4.7 66.6 1.0 CB A:ASP2146 4.7 95.5 1.0 C A:ASN2145 4.8 63.2 1.0 CG A:GLU2057 4.8 67.7 1.0 CA A:ASP2146 4.8 90.5 1.0 CB A:ILE2144 5.0 70.6 1.0 N A:SER2147 5.0 83.9 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC19-21 S2064P


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 S2064P within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2307 b:79.3 occ:1.00 O A:SER2147 2.2 80.2 1.0 OD2 A:ASP2239 2.2 72.3 1.0 OD1 A:ASP2177 2.4 74.6 1.0 OD2 A:ASP2179 2.5 77.2 1.0 OD1 A:ASN2145 2.6 63.1 1.0 OD2 A:ASP2177 2.8 71.7 1.0 CG A:ASP2177 3.0 71.3 1.0 CG A:ASP2239 3.3 72.2 1.0 C A:SER2147 3.4 79.3 1.0 CG A:ASN2145 3.6 63.8 1.0 CG A:ASP2179 3.6 79.1 1.0 CB A:ASP2239 3.8 70.9 1.0 N A:SER2147 3.9 83.9 1.0 ND2 A:ASN2145 4.0 64.8 1.0 CB A:ASP2179 4.0 78.0 1.0 O A:HIS2247 4.1 78.0 1.0 CA A:SER2147 4.2 81.9 1.0 OD1 A:ASP2239 4.4 73.7 1.0 N A:ARG2148 4.5 78.5 1.0 CB A:ASP2177 4.5 68.2 1.0 CB A:SER2147 4.6 80.6 1.0 CA A:ARG2148 4.6 75.5 1.0 CD A:PRO2149 4.6 68.3 1.0 OD1 A:ASP2179 4.7 81.6 1.0 C A:ASN2145 4.7 63.2 1.0 N A:ASP2146 4.7 89.7 1.0 C A:ARG2148 4.8 70.6 1.0 N A:PRO2149 4.8 67.6 1.0 CB A:ASN2145 4.9 64.7 1.0 C A:ASP2146 4.9 87.2 1.0 O A:ASN2145 5.0 64.6 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 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003