Calcium in PDB 4axw: Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2, Form I 2.2A.

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2, Form I 2.2A., PDB code: 4axw 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)	41.08 / 2.23
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.649, 40.468, 85.187, 90.00, 102.92, 90.00
R / Rfree (%)	17.459 / 23.634

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2, Form I 2.2A. 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 2.2A. (pdb code 4axw). 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 2.2A., PDB code: 4axw:
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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1209 b:22.7 occ:1.00 OD2 A:ASP41 2.2 19.7 1.0 O A:ARG5 2.3 30.3 1.0 OD2 A:ASP39 2.3 26.4 1.0 OD2 A:ASP87 2.3 20.4 1.0 OD1 A:ASN4 2.4 20.8 1.0 OD1 A:ASP37 2.5 24.2 1.0 OD2 A:ASP37 2.5 24.1 1.0 CG A:ASP37 2.9 25.1 1.0 CG A:ASN4 3.3 27.1 1.0 CG A:ASP41 3.3 19.2 1.0 CG A:ASP87 3.4 25.6 1.0 CG A:ASP39 3.4 28.0 1.0 C A:ARG5 3.5 28.8 1.0 ND2 A:ASN4 3.6 20.7 1.0 CB A:ASP39 3.8 25.5 1.0 CB A:ASP87 3.8 22.4 1.0 N A:ARG5 4.0 29.0 1.0 CB A:ASP41 4.0 20.8 1.0 CA A:ARG5 4.2 29.6 1.0 OD1 A:ASP41 4.3 20.0 1.0 O A:HOH2059 4.4 28.4 1.0 CB A:ASP37 4.4 22.0 1.0 O A:HOH2008 4.4 38.4 1.0 N A:LEU6 4.5 28.6 1.0 OD1 A:ASP87 4.5 25.0 1.0 OD1 A:ASP39 4.5 28.3 1.0 CA A:LEU6 4.6 27.6 1.0 CB A:ASN4 4.7 28.6 1.0 N A:ASP39 4.7 26.7 1.0 C A:ASN4 4.8 29.6 1.0 C A:LEU6 4.8 26.1 1.0 CB A:ARG5 4.8 29.3 1.0 CA A:ASP39 4.9 25.8 1.0 N A:PRO7 4.9 22.3 1.0 CA A:ASN4 4.9 29.4 1.0 CD A:PRO7 5.0 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1210 b:16.8 occ:1.00 OE2 A:GLU22 2.3 21.0 1.0 O A:VAL103 2.3 19.5 1.0 OD1 A:ASP105 2.3 17.6 1.0 OD1 A:ASP102 2.3 18.1 1.0 OE2 A:GLU74 2.4 22.3 1.0 OD1 A:ASP138 2.4 13.6 1.0 OE1 A:GLU74 2.7 18.8 1.0 CD A:GLU74 2.9 22.6 1.0 CG A:ASP102 3.3 22.1 1.0 CG A:ASP105 3.4 23.6 1.0 CD A:GLU22 3.4 23.8 1.0 C A:VAL103 3.5 20.2 1.0 CG A:ASP138 3.6 16.9 1.0 OD2 A:ASP102 3.8 19.6 1.0 N A:VAL103 3.9 21.0 1.0 N A:ASP105 3.9 21.5 1.0 OE1 A:GLU22 3.9 23.7 1.0 CA A:CA1211 3.9 23.2 1.0 OD2 A:ASP105 4.0 22.7 1.0 ND2 A:ASN106 4.1 21.5 1.0 CB A:ASP138 4.2 15.9 1.0 CA A:VAL103 4.3 19.6 1.0 CG A:GLU74 4.3 22.7 1.0 CA A:ASP138 4.4 16.6 1.0 N A:ASN104 4.5 19.7 1.0 NE A:ARG73 4.5 20.3 1.0 CB A:ASP102 4.6 20.7 1.0 CA A:ASN104 4.6 20.2 1.0 CA A:ASP102 4.6 21.1 1.0 OD2 A:ASP138 4.6 16.4 1.0 CB A:ASP105 4.6 21.7 1.0 C A:ASN104 4.7 20.9 1.0 CG A:GLU22 4.7 21.6 1.0 CA A:ASP105 4.7 21.1 1.0 C A:ASP102 4.7 21.6 1.0 CG2 A:VAL103 4.9 20.3 1.0 NH2 A:ARG73 5.0 21.4 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1211 b:23.2 occ:1.00 OD1 A:ASP72 2.2 24.3 1.0 OE1 A:GLU74 2.3 18.8 1.0 O A:HOH2086 2.3 20.1 1.0 OE1 A:GLU22 2.3 23.7 1.0 OD2 A:ASP105 2.4 22.7 1.0 O A:HOH2037 2.4 25.0 1.0 OD1 A:ASP105 3.0 17.6 1.0 CG A:ASP105 3.0 23.6 1.0 CD A:GLU22 3.2 23.8 1.0 CG A:ASP72 3.3 27.4 1.0 OE2 A:GLU22 3.5 21.0 1.0 CD A:GLU74 3.5 22.6 1.0 CA A:CA1210 3.9 16.8 1.0 OD2 A:ASP72 4.0 29.6 1.0 CA A:ASP72 4.1 25.4 1.0 CB A:ASP72 4.2 26.0 1.0 ND2 A:ASN106 4.2 21.5 1.0 N A:ARG73 4.2 24.8 1.0 O A:HOH2101 4.2 40.3 1.0 O A:HOH2085 4.3 33.9 1.0 OE2 A:GLU74 4.4 22.3 1.0 CG A:GLU74 4.4 22.7 1.0 N A:GLU74 4.4 26.1 1.0 O A:HOH2035 4.4 32.1 1.0 C A:ASP72 4.4 25.1 1.0 CB A:GLU74 4.4 27.2 1.0 CG A:GLU22 4.5 21.6 1.0 CB A:ASP105 4.5 21.7 1.0 O A:HOH2102 4.5 35.0 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1212 b:14.9 occ:1.00 OD2 A:ASP187 2.3 16.6 1.0 O A:ASN106 2.3 18.9 1.0 OD2 A:ASP136 2.3 14.9 1.0 OD2 A:ASP138 2.3 16.4 1.0 OD1 A:ASN104 2.3 15.9 1.0 O A:GLY142 2.4 18.7 1.0 OD1 A:ASP136 2.5 13.3 1.0 CG A:ASP136 2.7 19.2 1.0 CG A:ASP187 3.3 18.4 1.0 CG A:ASP138 3.3 16.9 1.0 C A:ASN106 3.4 18.6 1.0 CG A:ASN104 3.5 21.3 1.0 C A:GLY142 3.6 18.4 1.0 CB A:ASP138 3.7 15.9 1.0 CB A:ASP187 3.7 17.7 1.0 ND2 A:ASN104 3.9 14.7 1.0 N A:ASN106 4.1 19.7 1.0 CA A:ASN106 4.2 18.6 1.0 CB A:ASP136 4.2 18.4 1.0 CA A:GLY142 4.3 18.4 1.0 CB A:ASN106 4.3 19.0 1.0 OD1 A:ASP187 4.4 17.2 1.0 N A:ALA107 4.4 18.3 1.0 OD1 A:ASP138 4.5 13.6 1.0 CA A:ALA107 4.6 16.9 1.0 N A:GLY143 4.6 19.5 1.0 N A:ASP138 4.7 16.5 1.0 CB A:ASN104 4.7 18.6 1.0 CA A:ASP138 4.8 16.6 1.0 C A:ALA107 4.8 16.2 1.0 CA A:GLY143 4.8 19.2 1.0 CD1 A:LEU194 4.9 17.2 1.0 CA A:ASN104 5.0 20.2 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1237 b:21.8 occ:1.00 OD1 B:ASN120 2.2 31.7 1.0 OD2 B:ASP157 2.3 20.8 1.0 O B:ASN163 2.3 19.9 1.0 O B:ASN122 2.3 22.6 1.0 OD2 B:ASP215 2.4 19.6 1.0 OD2 B:ASP159 2.6 22.0 1.0 OD1 B:ASP157 2.6 24.4 1.0 CG B:ASP157 2.7 22.7 1.0 CG B:ASN120 3.3 29.5 1.0 C B:ASN122 3.4 23.8 1.0 CG B:ASP215 3.5 22.4 1.0 C B:ASN163 3.5 21.9 1.0 CG B:ASP159 3.6 27.3 1.0 ND2 B:ASN120 3.8 29.0 1.0 CB B:ASP215 3.8 19.2 1.0 CB B:ASP159 3.9 26.3 1.0 CA B:ASN122 4.2 24.7 1.0 CB B:ASP157 4.2 24.0 1.0 N B:ASN122 4.3 25.8 1.0 CA B:ASN163 4.3 22.4 1.0 CB B:ASN122 4.4 23.9 1.0 N B:GLY164 4.4 22.5 1.0 CB B:ASN163 4.5 22.8 1.0 N B:SER123 4.5 24.3 1.0 OD1 B:ASP215 4.5 23.8 1.0 CB B:ASN120 4.6 27.8 1.0 CA B:GLY164 4.6 23.1 1.0 CA B:ASN120 4.7 27.4 1.0 CA B:SER123 4.7 25.2 1.0 OD1 B:ASP159 4.8 24.7 1.0 CG B:ARG224 4.9 33.7 1.0 C B:ASN120 4.9 27.5 1.0 N B:ASP159 4.9 25.7 1.0 C B:SER123 5.0 24.7 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1238 b:28.6 occ:1.00 OD2 B:ASP85 2.3 19.9 1.0 OD1 B:ASP83 2.3 29.0 1.0 OE1 B:GLU27 2.4 22.6 1.0 OD2 B:ASP121 2.4 31.9 1.0 OE2 B:GLU28 2.4 30.8 1.0 O B:HOH2058 2.6 30.4 1.0 CG B:ASP121 3.3 28.3 1.0 CG B:ASP85 3.4 24.9 1.0 CG B:ASP83 3.4 30.2 1.0 CD B:GLU27 3.4 26.5 1.0 OD1 B:ASP121 3.5 26.0 1.0 CD B:GLU28 3.5 37.7 1.0 CG B:GLU28 3.9 36.0 1.0 OE2 B:GLU27 3.9 24.1 1.0 CA B:CA1239 4.0 23.2 1.0 CB B:ASP85 4.0 26.2 1.0 ND2 B:ASN122 4.1 21.7 1.0 OD2 B:ASP83 4.1 35.4 1.0 CA B:ASP83 4.3 28.1 1.0 N B:ASP85 4.3 25.0 1.0 CB B:ASP83 4.3 28.7 1.0 OD1 B:ASP85 4.3 22.4 1.0 N B:ARG84 4.4 24.4 1.0 O B:HOH2057 4.5 28.3 1.0 O B:HOH2016 4.5 43.2 1.0 OE1 B:GLU28 4.6 43.0 1.0 CG B:GLU27 4.6 27.0 1.0 C B:ASP83 4.7 26.2 1.0 CB B:ASP121 4.7 29.2 1.0 CA B:ASP85 4.8 26.1 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 2.2A.


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 2.2A. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1239 b:23.2 occ:1.00 OD1 B:ASP159 2.2 24.7 1.0 OE2 B:GLU27 2.3 24.1 1.0 OD1 B:ASP118 2.3 23.6 1.0 OD1 B:ASP85 2.3 22.4 1.0 OD1 B:ASP121 2.4 26.0 1.0 OD2 B:ASP85 2.5 19.9 1.0 O B:ARG119 2.5 25.7 1.0 CG B:ASP85 2.8 24.9 1.0 CD B:GLU27 3.3 26.5 1.0 CG B:ASP159 3.3 27.3 1.0 CG B:ASP118 3.4 24.4 1.0 CG B:ASP121 3.5 28.3 1.0 OE1 B:GLU27 3.6 22.6 1.0 C B:ARG119 3.6 26.4 1.0 N B:ARG119 3.8 24.1 1.0 ND2 B:ASN122 3.9 21.7 1.0 OD2 B:ASP121 4.0 31.9 1.0 CA B:CA1238 4.0 28.6 1.0 CB B:ASP159 4.0 26.3 1.0 OD2 B:ASP118 4.0 24.3 1.0 OD2 B:ASP159 4.3 22.0 1.0 N B:ASP121 4.3 28.2 1.0 CB B:ASP85 4.3 26.2 1.0 CA B:ARG119 4.3 27.0 1.0 CA B:ASP159 4.3 26.0 1.0 O B:HOH2059 4.5 37.2 1.0 CB B:ASP118 4.6 22.6 1.0 CA B:ASP118 4.6 23.5 1.0 CG B:GLU27 4.6 27.0 1.0 C B:ASP118 4.6 23.6 1.0 N B:ASN120 4.7 27.8 1.0 CB B:ARG119 4.7 28.8 1.0 CB B:ASP121 4.8 29.2 1.0 CA B:ASN120 4.9 27.4 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