Calcium in PDB 5tfk: Crystal Structure of Mouse Cadherin-23 EC19-21 Wt

The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 Wt, PDB code: 5tfk 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)	111.51 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.408, 66.932, 112.815, 90.00, 98.72, 90.00
R / Rfree (%)	20.1 / 24.4

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt (pdb code 5tfk). 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 Wt, PDB code: 5tfk:
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 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2301 b:88.5 occ:1.00 OD1 A:ASN1930 2.3 91.2 1.0 OD2 A:ASP1968 2.4 95.3 1.0 OD2 A:ASP2022 2.4 87.9 1.0 O A:TYR1972 2.4 95.1 1.0 O A:ASN1932 2.5 88.4 1.0 OD2 A:ASP1966 2.5 68.8 1.0 OD1 A:ASP1966 2.7 68.2 1.0 CG A:ASP1966 2.9 69.2 1.0 CG A:ASP2022 3.3 88.3 1.0 CG A:ASN1930 3.5 92.7 1.0 CG A:ASP1968 3.5 97.7 1.0 C A:ASN1932 3.6 91.5 1.0 CB A:ASP2022 3.6 87.3 1.0 C A:TYR1972 3.6 98.6 1.0 CB A:TYR1972 4.1 0.5 1.0 ND2 A:ASN1930 4.1 90.3 1.0 CB A:ASP1968 4.1 96.9 1.0 CA A:HIS1933 4.3 88.1 1.0 CA A:TYR1972 4.3 0.8 1.0 N A:HIS1933 4.3 91.0 1.0 OD1 A:ASP2022 4.4 87.1 1.0 CB A:ASP1966 4.4 70.0 1.0 OD1 A:ASP1968 4.5 98.7 1.0 CA A:ASN1932 4.5 92.7 1.0 N A:ASN1932 4.6 93.6 1.0 CB A:ASN1930 4.7 97.0 1.0 N A:ALA1973 4.7 98.0 1.0 CA A:ASN1930 4.8 99.2 1.0 CB A:ASN1932 4.9 89.2 1.0 C A:HIS1933 4.9 83.8 1.0 CA A:ALA1973 5.0 93.3 1.0 CD1 A:LEU2026 5.0 84.6 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2302 b:82.6 occ:1.00 OD2 A:ASP2041 2.1 77.3 1.0 OD1 A:ASP2005 2.3 88.9 1.0 O A:HOH2409 2.3 54.0 1.0 OE1 A:GLU2007 2.4 87.9 1.0 OE2 A:GLU1947 2.6 90.2 1.0 CG A:ASP2041 3.1 77.3 1.0 CG A:ASP2005 3.3 89.5 1.0 CD A:GLU1947 3.4 89.0 1.0 OD1 A:ASP2041 3.5 79.2 1.0 CD A:GLU2007 3.6 91.6 1.0 OE1 A:GLU1947 3.7 86.3 1.0 CA A:ASP2005 3.8 90.9 1.0 N A:ARG2006 3.8 90.0 1.0 CB A:ASP2005 3.9 89.2 1.0 ND2 A:ASN1948 4.1 90.8 1.0 C A:ASP2005 4.2 91.5 1.0 OD1 A:ASN1948 4.2 88.5 1.0 OD2 A:ASP2005 4.2 93.1 1.0 CA A:CA2303 4.4 77.4 1.0 CB A:ASP2041 4.4 76.2 1.0 OE2 A:GLU2007 4.5 92.7 1.0 N A:GLU2007 4.5 93.1 1.0 CG A:GLU2007 4.5 94.5 1.0 ND2 A:ASN2042 4.5 83.9 1.0 CG A:ASN1948 4.6 89.8 1.0 CG A:GLU1947 4.6 88.5 1.0 CB A:GLU2007 4.7 94.2 1.0 CA A:ARG2006 5.0 90.8 1.0 O A:ILE2004 5.0 93.7 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2303 b:77.4 occ:1.00 OE1 A:GLU1947 2.3 86.3 1.0 OD1 A:ASP2041 2.3 79.2 1.0 O A:ASP2039 2.4 88.7 1.0 OD1 A:ASP2038 2.4 95.7 1.0 OD1 A:ASP2074 2.5 81.0 1.0 OE2 A:GLU2007 2.9 92.7 1.0 OE1 A:GLU2007 3.0 87.9 1.0 CD A:GLU2007 3.2 91.6 1.0 CG A:ASP2074 3.3 83.5 1.0 CD A:GLU1947 3.4 89.0 1.0 CG A:ASP2041 3.4 77.3 1.0 C A:ASP2039 3.5 89.6 1.0 CG A:ASP2038 3.5 99.3 1.0 N A:ASP2039 3.7 90.0 1.0 OE2 A:GLU1947 3.9 90.2 1.0 OD2 A:ASP2041 4.0 77.3 1.0 CB A:ASP2074 4.0 86.0 1.0 N A:ASP2041 4.1 74.3 1.0 OD2 A:ASP2074 4.1 81.3 1.0 OD2 A:ASP2038 4.1 0.1 1.0 NE A:ARG2006 4.2 0.7 1.0 CA A:ASP2039 4.2 90.3 1.0 ND2 A:ASN2042 4.2 83.9 1.0 NH2 A:ARG2006 4.3 0.8 1.0 CA A:ASP2074 4.4 88.4 1.0 CA A:CA2302 4.4 82.6 1.0 CB A:ASP2041 4.5 76.2 1.0 C A:ASP2038 4.6 92.1 1.0 N A:ASN2040 4.6 90.8 1.0 CG A:GLU2007 4.6 94.5 1.0 CA A:ASP2038 4.6 92.2 1.0 CG A:GLU1947 4.6 88.5 1.0 CB A:ASP2038 4.7 96.6 1.0 CB A:ASP2039 4.7 88.7 1.0 CZ A:ARG2006 4.7 0.2 1.0 CA A:ASP2041 4.8 75.0 1.0 CA A:ASN2040 4.8 92.6 1.0 CB A:ARG2006 4.8 93.1 1.0 C A:ASN2040 4.9 91.9 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2304 b:91.0 occ:1.00 OE2 A:GLU2162 2.6 97.5 1.0 CD A:GLU2162 3.2 95.5 1.0 OD1 A:ASP2262 3.3 99.3 1.0 OD2 A:ASP2262 3.3 0.6 1.0 OE1 A:GLU2162 3.4 0.1 1.0 CG A:ASP2262 3.5 99.7 1.0 N A:VAL2263 4.0 91.9 1.0 C A:VAL2263 4.0 93.6 1.0 CG A:GLU2162 4.5 88.3 1.0 CA A:VAL2263 4.6 92.3 1.0 CB A:ASP2262 4.8 96.2 1.0 OD1 A:ASN2224 4.8 91.3 1.0 CA A:ASP2262 4.8 90.1 1.0 C A:ASP2262 4.9 89.2 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2305 b:81.3 occ:1.00 OD1 A:ASN2040 2.3 97.3 1.0 OD2 A:ASP2125 2.3 84.7 1.0 OD2 A:ASP2072 2.4 83.3 1.0 O A:ASN2042 2.4 82.2 1.0 OD2 A:ASP2074 2.5 81.3 1.0 O A:ASN2078 2.5 84.3 1.0 OD1 A:ASP2072 2.8 91.6 1.0 CG A:ASP2072 3.0 88.1 1.0 CG A:ASN2040 3.4 99.0 1.0 CG A:ASP2125 3.4 85.1 1.0 CG A:ASP2074 3.5 83.5 1.0 C A:ASN2042 3.6 81.4 1.0 C A:ASN2078 3.7 88.6 1.0 CB A:ASP2074 3.8 86.0 1.0 CB A:ASP2125 4.0 87.0 1.0 ND2 A:ASN2040 4.0 0.7 1.0 N A:ASN2042 4.1 78.7 1.0 CA A:ASN2042 4.3 80.4 1.0 CA A:ASN2078 4.4 89.9 1.0 OD1 A:ASP2125 4.4 85.7 1.0 CB A:ASN2078 4.4 89.7 1.0 CB A:ASN2042 4.5 81.4 1.0 CB A:ASP2072 4.5 88.2 1.0 CD A:PRO2044 4.5 81.3 1.0 CD1 A:LEU2131 4.5 77.8 1.0 CA A:ASN2040 4.5 92.6 1.0 CB A:ASN2040 4.6 96.2 1.0 C A:ASN2040 4.6 91.9 1.0 N A:TRP2043 4.6 83.1 1.0 OD1 A:ASP2074 4.7 81.0 1.0 N A:GLY2079 4.7 92.1 1.0 N A:ASP2041 4.8 74.3 1.0 CB A:LEU2131 4.8 81.2 1.0 CA A:TRP2043 4.9 83.0 1.0 O A:ASN2040 5.0 93.5 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2306 b:77.4 occ:1.00 O A:HOH2401 2.2 62.8 1.0 OD1 A:ASP2110 2.2 73.0 1.0 OE2 A:GLU2112 2.3 76.9 1.0 OD1 A:ASP2146 2.4 86.5 1.0 OD2 A:ASP2146 2.5 91.2 1.0 OE1 A:GLU2057 2.5 70.5 1.0 CG A:ASP2146 2.8 88.7 1.0 CG A:ASP2110 3.2 75.1 1.0 CA A:CA2307 3.4 69.2 1.0 CD A:GLU2112 3.4 75.1 1.0 CD A:GLU2057 3.5 71.1 1.0 OE2 A:GLU2057 3.7 69.9 1.0 OD2 A:ASP2110 3.8 74.2 1.0 CG A:GLU2112 4.2 74.7 1.0 CB A:GLU2112 4.2 74.9 1.0 N A:GLU2112 4.2 74.7 1.0 CB A:ASP2146 4.3 89.3 1.0 OE1 A:GLU2112 4.3 77.3 1.0 CB A:ASP2110 4.4 77.0 1.0 N A:ARG2111 4.4 74.0 1.0 CA A:ASP2110 4.5 76.1 1.0 OD1 A:ASP2179 4.6 80.5 1.0 C A:ASP2110 4.7 76.1 1.0 CB A:SER2147 4.8 77.1 1.0 OD1 A:ASN2058 4.8 82.5 1.0 C A:ASP2146 4.8 81.6 1.0 CG A:GLU2057 4.8 73.3 1.0 O A:ILE2144 4.8 72.4 1.0 CA A:GLU2112 4.9 74.7 1.0 ND2 A:ASN2058 4.9 83.9 1.0 O A:ASP2146 4.9 84.5 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2307 b:69.2 occ:1.00 OE2 A:GLU2112 2.2 76.9 1.0 O A:ILE2144 2.3 72.4 1.0 OD1 A:ASP2179 2.3 80.5 1.0 OD1 A:ASP2143 2.3 77.7 1.0 OE2 A:GLU2057 2.3 69.9 1.0 OD1 A:ASP2146 2.6 86.5 1.0 OE1 A:GLU2112 2.8 77.3 1.0 CD A:GLU2112 2.8 75.1 1.0 CD A:GLU2057 3.3 71.1 1.0 CG A:ASP2143 3.3 76.4 1.0 CA A:CA2306 3.4 77.4 1.0 C A:ILE2144 3.5 73.7 1.0 CG A:ASP2179 3.5 78.5 1.0 CG A:ASP2146 3.6 88.7 1.0 OE1 A:GLU2057 3.6 70.5 1.0 OD2 A:ASP2143 3.9 79.3 1.0 N A:ASP2146 4.0 83.1 1.0 N A:ILE2144 4.0 74.4 1.0 OD2 A:ASP2146 4.1 91.2 1.0 CB A:ASP2179 4.3 77.2 1.0 CG A:GLU2112 4.3 74.7 1.0 N A:ASN2145 4.4 73.1 1.0 NE A:ARG2111 4.4 77.3 1.0 CA A:ILE2144 4.4 76.2 1.0 OD2 A:ASP2179 4.4 78.1 1.0 CA A:ASN2145 4.4 71.8 1.0 CB A:ASP2143 4.4 76.8 1.0 CA A:ASP2179 4.5 75.8 1.0 CA A:ASP2143 4.5 75.8 1.0 CB A:ARG2111 4.5 74.9 1.0 CB A:ASP2146 4.6 89.3 1.0 CG A:GLU2057 4.6 73.3 1.0 C A:ASP2143 4.7 75.7 1.0 C A:ASN2145 4.7 70.7 1.0 CA A:ASP2146 4.8 84.8 1.0 CB A:SER2147 4.9 77.1 1.0 N A:SER2147 5.0 79.3 1.0 O A:HOH2401 5.0 62.8 1.0 OD1 A:ASP2110 5.0 73.0 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Mouse Cadherin-23 EC19-21 Wt


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 Wt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2308 b:78.8 occ:1.00 O A:SER2147 2.1 78.8 1.0 OD2 A:ASP2239 2.4 77.6 1.0 OD1 A:ASP2177 2.4 72.3 1.0 OD1 A:ASN2145 2.5 76.4 1.0 OD2 A:ASP2177 2.6 69.1 1.0 OD2 A:ASP2179 2.6 78.1 1.0 CG A:ASP2177 2.9 69.6 1.0 C A:SER2147 3.3 76.3 1.0 CG A:ASP2239 3.4 77.8 1.0 CG A:ASN2145 3.5 73.5 1.0 CB A:ASP2239 3.7 74.8 1.0 CG A:ASP2179 3.8 78.5 1.0 N A:SER2147 3.9 79.3 1.0 ND2 A:ASN2145 3.9 76.0 1.0 CA A:SER2147 4.1 77.8 1.0 O A:HIS2247 4.1 75.0 1.0 CB A:ASP2179 4.2 77.2 1.0 OG A:SER2242 4.2 87.3 1.0 N A:ARG2148 4.3 75.7 1.0 CB A:ASP2177 4.4 67.7 1.0 CA A:ARG2148 4.4 72.6 1.0 CD A:PRO2149 4.5 63.3 1.0 CB A:SER2147 4.5 77.1 1.0 OD1 A:ASP2239 4.5 79.3 1.0 C A:ASN2145 4.6 70.7 1.0 N A:PRO2149 4.7 63.3 1.0 C A:ARG2148 4.7 66.5 1.0 N A:ASP2146 4.8 83.1 1.0 O A:ASN2145 4.8 71.2 1.0 CB A:ASN2145 4.8 72.9 1.0 CB A:SER2242 4.8 83.4 1.0 OD1 A:ASP2179 4.9 80.5 1.0 C A:ASP2146 5.0 81.6 1.0 CA A:ASN2145 5.0 71.8 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