Calcium in PDB 4apx: Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I, PDB code: 4apx 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)	32.03 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.606, 40.469, 84.623, 90.00, 103.12, 90.00
R / Rfree (%)	16.138 / 19.307

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I (pdb code 4apx). 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 EC1-2 and Protocadherin-15 EC1-2 Form I, PDB code: 4apx:
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 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1209 b:17.6 occ:1.00 O A:ARG5 2.3 20.3 1.0 OD2 A:ASP41 2.4 18.8 1.0 OD2 A:ASP39 2.4 19.7 1.0 OD2 A:ASP87 2.4 17.7 1.0 OD1 A:ASN4 2.5 20.9 1.0 OD2 A:ASP37 2.5 19.1 1.0 OD1 A:ASP37 2.6 20.4 1.0 CG A:ASP37 2.9 18.1 1.0 CG A:ASN4 3.4 20.6 1.0 CG A:ASP87 3.4 19.4 1.0 CG A:ASP41 3.4 18.5 1.0 CG A:ASP39 3.4 21.1 1.0 C A:ARG5 3.5 21.1 1.0 ND2 A:ASN4 3.7 20.9 1.0 CB A:ASP39 3.7 20.6 1.0 CB A:ASP87 3.8 18.5 1.0 N A:ARG5 4.0 21.9 1.0 CB A:ASP41 4.0 17.3 1.0 CA A:ARG5 4.3 22.1 1.0 OD1 A:ASP41 4.3 18.0 1.0 O A:HOH2133 4.3 24.1 1.0 O A:HOH2014 4.4 24.2 1.0 CB A:ASP37 4.4 18.6 1.0 N A:LEU6 4.4 20.8 1.0 OD1 A:ASP87 4.5 17.8 1.0 CA A:LEU6 4.5 20.3 1.0 OD1 A:ASP39 4.6 23.5 1.0 N A:ASP39 4.6 20.8 1.0 CB A:ARG5 4.7 22.4 1.0 CB A:ASN4 4.7 22.4 1.0 C A:LEU6 4.7 19.9 1.0 CA A:ASP39 4.8 20.5 1.0 C A:ASN4 4.8 22.5 1.0 CD A:PRO7 4.8 18.4 1.0 N A:PRO7 4.9 18.3 1.0 CA A:ASN4 4.9 23.0 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1210 b:13.9 occ:1.00 OD1 A:ASP138 2.3 14.1 1.0 OD1 A:ASP102 2.3 14.4 1.0 OE2 A:GLU22 2.4 15.9 1.0 O A:VAL103 2.4 15.8 1.0 OD1 A:ASP105 2.4 14.4 1.0 OE2 A:GLU74 2.4 16.4 1.0 OE1 A:GLU74 2.6 16.8 1.0 CD A:GLU74 2.9 16.6 1.0 CG A:ASP102 3.4 15.3 1.0 CD A:GLU22 3.4 16.0 1.0 CG A:ASP105 3.4 16.5 1.0 CG A:ASP138 3.5 13.6 1.0 C A:VAL103 3.6 15.3 1.0 OD2 A:ASP102 3.8 15.8 1.0 OE1 A:GLU22 3.8 16.3 1.0 CA A:CA1211 3.9 16.1 1.0 N A:VAL103 3.9 15.7 1.0 N A:ASP105 3.9 14.5 1.0 OD2 A:ASP105 4.0 17.3 1.0 ND2 A:ASN106 4.0 12.8 1.0 CB A:ASP138 4.2 12.9 1.0 CG A:GLU74 4.3 19.4 1.0 CA A:ASP138 4.4 12.9 1.0 CA A:VAL103 4.4 15.8 1.0 OD2 A:ASP138 4.4 12.4 1.0 NE A:ARG73 4.5 18.9 1.0 CB A:ASP105 4.5 15.3 1.0 CB A:ASP102 4.6 14.8 1.0 N A:ASN104 4.6 14.7 1.0 CA A:ASN104 4.6 14.1 1.0 CA A:ASP105 4.7 14.7 1.0 CA A:ASP102 4.7 15.9 1.0 CG A:GLU22 4.7 16.0 1.0 C A:ASN104 4.7 14.7 1.0 C A:ASP102 4.8 16.0 1.0 CG2 A:VAL103 4.8 16.4 1.0 NH2 A:ARG73 4.9 19.3 1.0 CB A:ARG73 4.9 19.8 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1211 b:16.1 occ:1.00 OE1 A:GLU74 2.3 16.8 1.0 OD1 A:ASP72 2.4 18.4 1.0 OE1 A:GLU22 2.4 16.3 1.0 OD2 A:ASP105 2.4 17.3 1.0 O A:HOH2214 2.4 17.8 1.0 O A:HOH2069 2.4 18.3 1.0 OD1 A:ASP105 2.9 14.4 1.0 CG A:ASP105 3.0 16.5 1.0 CD A:GLU22 3.3 16.0 1.0 CG A:ASP72 3.4 21.5 1.0 CD A:GLU74 3.6 16.6 1.0 OE2 A:GLU22 3.6 15.9 1.0 CA A:CA1210 3.9 13.9 1.0 N A:ARG73 4.1 19.5 1.0 CA A:ASP72 4.1 21.0 1.0 OD2 A:ASP72 4.2 22.1 1.0 CB A:ASP72 4.2 21.2 1.0 ND2 A:ASN106 4.2 12.8 1.0 N A:GLU74 4.2 21.4 1.0 O A:HOH2213 4.3 25.1 1.0 CB A:GLU74 4.3 21.8 1.0 O A:HOH2259 4.4 28.1 1.0 CG A:GLU74 4.4 19.4 1.0 C A:ASP72 4.4 20.8 1.0 OE2 A:GLU74 4.4 16.4 1.0 CB A:ASP105 4.4 15.3 1.0 O A:HOH2066 4.5 23.9 1.0 CG A:GLU22 4.5 16.0 1.0 O A:HOH2215 4.5 41.9 1.0 O A:HOH2260 4.5 35.5 1.0 O A:HOH2067 4.6 25.1 1.0 CA A:GLU74 4.9 22.6 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1212 b:12.5 occ:1.00 O A:ASN106 2.3 13.7 1.0 O A:GLY142 2.3 12.5 1.0 OD2 A:ASP136 2.4 12.8 1.0 OD1 A:ASN104 2.4 12.8 1.0 OD2 A:ASP187 2.4 13.0 1.0 OD2 A:ASP138 2.4 12.4 1.0 OD1 A:ASP136 2.5 12.4 1.0 CG A:ASP136 2.8 12.8 1.0 CG A:ASP187 3.4 12.7 1.0 CG A:ASP138 3.4 13.6 1.0 C A:ASN106 3.4 12.4 1.0 CG A:ASN104 3.4 13.9 1.0 C A:GLY142 3.5 11.9 1.0 CB A:ASP138 3.6 12.9 1.0 CB A:ASP187 3.7 12.7 1.0 ND2 A:ASN104 3.8 13.0 1.0 CA A:GLY142 4.1 12.6 1.0 N A:ASN106 4.1 13.3 1.0 CA A:ASN106 4.2 12.8 1.0 CB A:ASP136 4.2 12.9 1.0 CB A:ASN106 4.4 13.2 1.0 OD1 A:ASP187 4.4 11.4 1.0 N A:ALA107 4.4 12.9 1.0 N A:GLY143 4.5 12.4 1.0 OD1 A:ASP138 4.5 14.1 1.0 CA A:ALA107 4.6 13.1 1.0 N A:ASP138 4.7 13.3 1.0 CB A:ASN104 4.7 13.1 1.0 CA A:ASP138 4.8 12.9 1.0 CA A:GLY143 4.8 12.0 1.0 C A:ALA107 4.9 13.0 1.0 CB A:LEU194 4.9 14.4 1.0 CD1 A:LEU194 4.9 14.0 1.0 CA A:ASN104 4.9 14.1 1.0 N A:ASP105 5.0 14.5 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1238 b:18.7 occ:1.00 OD1 B:ASN120 2.3 19.2 1.0 O B:ASN122 2.4 19.4 1.0 O B:ASN163 2.4 19.5 1.0 OD2 B:ASP159 2.4 18.5 1.0 OD2 B:ASP215 2.4 18.1 1.0 OD2 B:ASP157 2.4 19.2 1.0 OD1 B:ASP157 2.6 21.5 1.0 CG B:ASP157 2.8 19.9 1.0 CG B:ASP215 3.4 17.7 1.0 CG B:ASN120 3.4 20.2 1.0 CG B:ASP159 3.4 18.8 1.0 C B:ASN122 3.5 20.0 1.0 C B:ASN163 3.5 19.1 1.0 CB B:ASP215 3.8 17.4 1.0 CB B:ASP159 3.8 19.6 1.0 ND2 B:ASN120 3.9 18.5 1.0 CA B:ASN122 4.3 20.2 1.0 N B:ASN122 4.3 20.6 1.0 CB B:ASP157 4.3 18.9 1.0 CA B:ASN163 4.4 19.4 1.0 N B:SER123 4.5 20.3 1.0 CB B:ASN163 4.5 19.5 1.0 CB B:ASN122 4.5 20.5 1.0 N B:GLY164 4.5 19.0 1.0 OD1 B:ASP215 4.5 17.5 1.0 OD1 B:ASP159 4.5 19.1 1.0 CD B:ARG224 4.6 28.7 1.0 CA B:GLY164 4.6 19.6 1.0 CA B:SER123 4.6 20.6 1.0 CB B:ASN120 4.7 20.6 1.0 CA B:ASN120 4.8 20.5 1.0 C B:ASN120 4.9 21.2 1.0 N B:ASP159 4.9 19.8 1.0 C B:SER123 4.9 20.3 1.0 CA B:ASP159 5.0 19.9 1.0 CD B:PRO124 5.0 20.1 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1239 b:23.3 occ:1.00 OD2 B:ASP85 2.3 20.1 1.0 OD2 B:ASP121 2.3 24.6 1.0 OE1 B:GLU27 2.3 20.1 1.0 OD1 B:ASP83 2.4 25.2 1.0 OE2 B:GLU28 2.4 28.6 1.0 O B:HOH2063 2.5 22.6 1.0 CG B:ASP121 3.2 22.4 1.0 CD B:GLU27 3.3 22.5 1.0 OD1 B:ASP121 3.3 21.8 1.0 CG B:ASP83 3.4 25.4 1.0 CD B:GLU28 3.4 31.4 1.0 CG B:ASP85 3.4 22.6 1.0 OE2 B:GLU27 3.6 20.0 1.0 CG B:GLU28 3.9 29.3 1.0 CB B:ASP85 4.0 24.0 1.0 CA B:CA1240 4.0 20.3 1.0 OD2 B:ASP83 4.1 27.0 1.0 ND2 B:ASN122 4.2 20.8 1.0 N B:ASP85 4.3 23.4 1.0 CB B:ASP83 4.3 23.9 1.0 N B:ARG84 4.3 22.5 1.0 CA B:ASP83 4.3 23.8 1.0 OD1 B:ASP85 4.4 22.6 1.0 OE1 B:GLU28 4.4 34.5 1.0 O B:HOH2194 4.4 30.7 1.0 CG B:GLU27 4.5 21.5 1.0 O B:HOH2062 4.6 38.3 1.0 CB B:ASP121 4.6 22.2 1.0 O B:HOH2232 4.7 43.5 1.0 C B:ASP83 4.8 23.0 1.0 O B:HOH2061 4.8 44.9 1.0 CA B:ASP85 4.8 24.0 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form I


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 EC1-2 and Protocadherin-15 EC1-2 Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1240 b:20.3 occ:1.00 OD1 B:ASP118 2.3 18.5 1.0 OE2 B:GLU27 2.3 20.0 1.0 OD1 B:ASP159 2.3 19.1 1.0 OD1 B:ASP121 2.4 21.8 1.0 OD2 B:ASP85 2.5 20.1 1.0 OD1 B:ASP85 2.5 22.6 1.0 O B:ARG119 2.5 20.4 1.0 CG B:ASP85 2.8 22.6 1.0 CG B:ASP159 3.4 18.8 1.0 CG B:ASP118 3.4 19.9 1.0 CD B:GLU27 3.4 22.5 1.0 CG B:ASP121 3.6 22.4 1.0 C B:ARG119 3.7 20.9 1.0 N B:ARG119 3.8 20.4 1.0 OE1 B:GLU27 3.8 20.1 1.0 OD2 B:ASP118 4.0 20.7 1.0 CB B:ASP159 4.0 19.6 1.0 ND2 B:ASN122 4.0 20.8 1.0 CA B:CA1239 4.0 23.3 1.0 OD2 B:ASP121 4.2 24.6 1.0 N B:ASP121 4.2 20.3 1.0 CA B:ASP159 4.2 19.9 1.0 O B:HOH2198 4.2 25.5 1.0 OD2 B:ASP159 4.3 18.5 1.0 CA B:ARG119 4.3 21.5 1.0 CB B:ASP85 4.3 24.0 1.0 CB B:ASP118 4.5 20.1 1.0 CA B:ASP118 4.6 19.9 1.0 C B:ASP118 4.6 20.4 1.0 CG B:GLU27 4.7 21.5 1.0 N B:ASN120 4.7 20.4 1.0 CB B:ASP121 4.7 22.2 1.0 CB B:ARG119 4.8 22.6 1.0 CA B:ASN120 4.9 20.5 1.0 CA B:ASP121 4.9 21.4 1.0

M.Sotomayor, W.Weihofen, R.Gaudet, D.P.Corey. Structure of A Force-Conveying Cadherin Bond Essential For Inner-Ear Mechanotransduction Nature V. 492 128 2012.
ISSN: ISSN 0028-0836
PubMed: 23135401
DOI: 10.1038/NATURE11590