Calcium in PDB 4aq8: Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II, PDB code: 4aq8 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)	38.57 / 2.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.749, 57.030, 156.164, 90.00, 98.92, 90.00
R / Rfree (%)	18.854 / 24.273

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II (pdb code 4aq8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II, PDB code: 4aq8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1209 b:33.2 occ:1.00 OD2 A:ASP41 2.3 37.2 1.0 OD2 A:ASP39 2.3 36.7 1.0 OD1 A:ASN4 2.3 45.8 1.0 OD2 A:ASP87 2.4 38.1 1.0 O A:ARG5 2.4 39.9 1.0 OD2 A:ASP37 2.4 31.7 1.0 OD1 A:ASP37 2.7 28.3 1.0 CG A:ASP37 2.9 30.4 1.0 CG A:ASN4 3.4 49.2 1.0 CG A:ASP39 3.4 34.4 1.0 CG A:ASP87 3.5 40.0 1.0 CG A:ASP41 3.5 35.5 1.0 C A:ARG5 3.5 41.1 1.0 ND2 A:ASN4 3.8 47.7 1.0 CB A:ASP39 3.8 33.4 1.0 CB A:ASP87 3.9 39.1 1.0 N A:ARG5 4.0 46.0 1.0 CB A:ASP41 4.1 33.0 1.0 CA A:ARG5 4.3 43.5 1.0 N A:LEU6 4.4 40.6 1.0 CB A:ASP37 4.4 28.8 1.0 OD1 A:ASP41 4.5 37.2 1.0 CA A:LEU6 4.5 38.8 1.0 OD1 A:ASP87 4.5 41.6 1.0 OD1 A:ASP39 4.5 35.6 1.0 CD A:PRO7 4.7 34.5 1.0 CB A:ASN4 4.7 52.5 1.0 C A:LEU6 4.8 35.7 1.0 N A:ASP39 4.8 31.9 1.0 C A:ASN4 4.9 50.0 1.0 N A:PRO7 4.9 33.9 1.0 CB A:ARG5 4.9 42.1 1.0 CA A:ASP39 4.9 32.3 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1210 b:32.7 occ:1.00 OE2 A:GLU22 2.0 36.6 1.0 OE1 A:GLU74 2.2 36.3 1.0 O A:HOH2053 2.3 3.0 1.0 OD1 A:ASP72 2.4 38.1 1.0 O A:HOH2016 2.4 19.2 1.0 OD2 A:ASP105 2.5 32.9 1.0 OD1 A:ASP105 3.0 27.9 1.0 CD A:GLU22 3.1 35.1 1.0 CG A:ASP105 3.1 31.4 1.0 CG A:ASP72 3.3 38.8 1.0 CD A:GLU74 3.4 35.2 1.0 OE1 A:GLU22 3.7 33.9 1.0 OD2 A:ASP72 3.9 39.5 1.0 O A:HOH2050 3.9 4.6 1.0 CA A:CA1211 3.9 30.0 1.0 CG A:GLU22 4.1 34.6 1.0 O A:HOH2065 4.1 17.3 1.0 CB A:ASP72 4.2 37.8 1.0 CA A:ASP72 4.3 35.3 1.0 ND2 A:ASN106 4.3 30.4 1.0 OE2 A:GLU74 4.3 34.1 1.0 N A:ARG73 4.3 32.3 1.0 CG A:GLU74 4.3 37.0 1.0 CB A:GLU74 4.3 37.8 1.0 N A:GLU74 4.4 34.3 1.0 CB A:ASP105 4.6 31.3 1.0 C A:ASP72 4.6 33.9 1.0 O A:HOH2066 4.8 9.1 1.0 O A:HOH2028 4.8 24.0 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1211 b:30.0 occ:1.00 OD1 A:ASP102 2.2 30.7 1.0 OD1 A:ASP138 2.3 25.8 1.0 O A:VAL103 2.3 28.3 1.0 OE2 A:GLU74 2.4 34.1 1.0 OD1 A:ASP105 2.4 27.9 1.0 OE1 A:GLU22 2.6 33.9 1.0 OE1 A:GLU74 2.8 36.3 1.0 CD A:GLU74 3.0 35.2 1.0 CG A:ASP102 3.2 29.4 1.0 CG A:ASP105 3.4 31.4 1.0 CD A:GLU22 3.5 35.1 1.0 CG A:ASP138 3.6 25.8 1.0 C A:VAL103 3.6 28.5 1.0 OE2 A:GLU22 3.7 36.6 1.0 OD2 A:ASP102 3.7 28.0 1.0 N A:VAL103 3.9 30.0 1.0 ND2 A:ASN106 3.9 30.4 1.0 N A:ASP105 3.9 28.7 1.0 OD2 A:ASP105 3.9 32.9 1.0 CA A:CA1210 3.9 32.7 1.0 CB A:ASP138 4.3 24.7 1.0 CA A:VAL103 4.4 29.4 1.0 CB A:ASP102 4.4 29.9 1.0 CG A:GLU74 4.4 37.0 1.0 CA A:ASP138 4.5 25.7 1.0 CB A:ASP105 4.5 31.3 1.0 OD2 A:ASP138 4.5 24.6 1.0 N A:ASN104 4.5 28.4 1.0 CA A:ASN104 4.6 27.7 1.0 CA A:ASP102 4.6 31.1 1.0 CA A:ASP105 4.6 29.4 1.0 C A:ASP102 4.7 30.6 1.0 NH2 A:ARG73 4.7 33.8 1.0 C A:ASN104 4.7 28.4 1.0 O A:HOH2053 4.7 3.0 1.0 NE A:ARG73 4.7 29.9 1.0 CG2 A:VAL103 4.8 30.1 1.0 CB A:ARG73 4.8 30.4 1.0 CG A:GLU22 4.8 34.6 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1212 b:20.9 occ:1.00 OD1 A:ASN104 2.2 25.6 1.0 O A:ASN106 2.2 24.4 1.0 OD2 A:ASP136 2.3 26.0 1.0 O A:GLY142 2.3 22.6 1.0 OD2 A:ASP187 2.4 25.2 1.0 OD2 A:ASP138 2.4 24.6 1.0 OD1 A:ASP136 2.6 25.4 1.0 CG A:ASP136 2.8 25.8 1.0 CG A:ASN104 3.3 26.6 1.0 CG A:ASP138 3.3 25.8 1.0 CG A:ASP187 3.4 24.3 1.0 C A:ASN106 3.4 25.6 1.0 C A:GLY142 3.5 23.3 1.0 CB A:ASP138 3.6 24.7 1.0 CB A:ASP187 3.8 22.5 1.0 ND2 A:ASN104 3.8 28.1 1.0 N A:ASN106 4.2 27.2 1.0 CA A:ASN106 4.2 27.1 1.0 CA A:GLY142 4.2 23.7 1.0 CB A:ASP136 4.3 24.9 1.0 CB A:ASN106 4.3 27.6 1.0 OD1 A:ASP187 4.5 25.7 1.0 OD1 A:ASP138 4.5 25.8 1.0 N A:ALA107 4.5 26.0 1.0 CB A:ASN104 4.5 27.1 1.0 N A:GLY143 4.5 24.2 1.0 CA A:ALA107 4.7 24.5 1.0 N A:ASP138 4.7 25.8 1.0 CA A:GLY143 4.8 24.8 1.0 CA A:ASP138 4.8 25.7 1.0 CA A:ASN104 4.8 27.7 1.0 C A:ALA107 5.0 24.1 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1209 b:40.6 occ:1.00 OD1 B:ASN4 2.2 49.2 1.0 OD2 B:ASP37 2.2 47.0 1.0 OD2 B:ASP87 2.3 39.6 1.0 O B:ARG5 2.4 45.1 1.0 OD2 B:ASP41 2.4 40.7 1.0 OD2 B:ASP39 2.4 48.8 1.0 OD1 B:ASP37 2.7 49.2 1.0 CG B:ASP37 2.8 46.7 1.0 CG B:ASN4 3.2 49.6 1.0 C B:ARG5 3.5 46.4 1.0 CG B:ASP41 3.5 43.8 1.0 CG B:ASP87 3.5 40.8 1.0 CG B:ASP39 3.5 51.6 1.0 ND2 B:ASN4 3.7 48.7 1.0 N B:ARG5 3.8 50.9 1.0 CB B:ASP39 4.0 51.6 1.0 CB B:ASP41 4.0 43.1 1.0 CB B:ASP87 4.1 40.3 1.0 CA B:ARG5 4.2 49.9 1.0 CB B:ASP37 4.3 45.5 1.0 N B:LEU6 4.4 45.2 1.0 CB B:ASN4 4.4 52.5 1.0 OD1 B:ASP41 4.5 45.5 1.0 OD1 B:ASP87 4.5 41.8 1.0 C B:ASN4 4.6 52.8 1.0 CA B:LEU6 4.6 42.4 1.0 OD1 B:ASP39 4.6 54.5 1.0 N B:ASP39 4.6 51.3 1.0 CA B:ASN4 4.7 54.1 1.0 C B:LEU6 4.8 41.2 1.0 CB B:ARG5 4.9 51.3 1.0 CA B:ASP39 4.9 52.3 1.0 CD B:PRO7 5.0 38.7 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1210 b:26.9 occ:1.00 O B:HOH2024 2.2 11.6 1.0 OE1 B:GLU74 2.2 25.8 1.0 OD2 B:ASP105 2.3 27.0 1.0 OE1 B:GLU22 2.3 25.8 1.0 OD1 B:ASP72 2.3 26.9 1.0 O B:HOH2059 2.3 2.9 1.0 CG B:ASP105 3.1 26.0 1.0 OD1 B:ASP105 3.1 23.5 1.0 CD B:GLU22 3.2 26.2 1.0 CG B:ASP72 3.4 28.1 1.0 CD B:GLU74 3.5 26.8 1.0 OE2 B:GLU22 3.5 26.9 1.0 CA B:CA1212 3.8 24.3 1.0 O B:HOH2060 4.0 13.6 1.0 OD2 B:ASP72 4.1 27.9 1.0 ND2 B:ASN106 4.1 26.2 1.0 CA B:ASP72 4.2 25.5 1.0 O B:HOH2072 4.2 16.4 1.0 N B:GLU74 4.3 27.3 1.0 CG B:GLU74 4.3 29.8 1.0 N B:ARG73 4.3 24.5 1.0 CB B:ASP72 4.3 27.1 1.0 CB B:GLU74 4.3 29.8 1.0 OE2 B:GLU74 4.4 26.2 1.0 O B:HOH2022 4.4 12.8 1.0 O B:HOH2073 4.5 22.3 1.0 C B:ASP72 4.5 25.2 1.0 CB B:ASP105 4.5 26.5 1.0 CG B:GLU22 4.5 25.9 1.0 CA B:GLU74 5.0 28.8 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1211 b:23.0 occ:1.00 OD1 B:ASN104 2.2 22.2 1.0 OD2 B:ASP138 2.3 23.2 1.0 O B:GLY142 2.3 23.6 1.0 OD1 B:ASP136 2.4 24.1 1.0 OD2 B:ASP136 2.4 23.0 1.0 O B:ASN106 2.4 23.6 1.0 OD2 B:ASP187 2.4 22.9 1.0 CG B:ASP136 2.7 23.9 1.0 CG B:ASN104 3.3 25.4 1.0 CG B:ASP138 3.3 22.6 1.0 CG B:ASP187 3.4 25.7 1.0 C B:GLY142 3.5 24.1 1.0 C B:ASN106 3.6 24.7 1.0 CB B:ASP138 3.6 22.5 1.0 CB B:ASP187 3.7 25.2 1.0 ND2 B:ASN104 3.8 25.2 1.0 CB B:ASP136 4.2 23.5 1.0 N B:ASN106 4.3 24.5 1.0 CA B:GLY142 4.3 24.5 1.0 CA B:ASN106 4.3 24.9 1.0 CB B:ASN106 4.3 24.6 1.0 OD1 B:ASP138 4.5 22.4 1.0 OD1 B:ASP187 4.5 26.0 1.0 N B:GLY143 4.6 25.0 1.0 N B:ALA107 4.6 26.0 1.0 CB B:ASN104 4.6 25.8 1.0 N B:ASP138 4.7 22.4 1.0 CA B:ASP138 4.7 22.7 1.0 CA B:GLY143 4.7 25.1 1.0 CA B:ALA107 4.8 26.1 1.0 CD1 B:LEU194 4.8 34.4 1.0 CA B:ASN104 4.9 25.8 1.0 CB B:LEU194 4.9 32.2 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


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 EC1-2 and Protocadherin-15 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1212 b:24.3 occ:1.00 OD1 B:ASP102 2.2 25.0 1.0 OD1 B:ASP105 2.3 23.5 1.0 OD1 B:ASP138 2.3 22.4 1.0 O B:VAL103 2.3 27.0 1.0 OE2 B:GLU22 2.4 26.9 1.0 OE2 B:GLU74 2.5 26.2 1.0 OE1 B:GLU74 2.6 25.8 1.0 CD B:GLU74 2.9 26.8 1.0 CG B:ASP102 3.3 25.6 1.0 CG B:ASP105 3.4 26.0 1.0 CG B:ASP138 3.5 22.6 1.0 CD B:GLU22 3.5 26.2 1.0 C B:VAL103 3.5 27.4 1.0 OD2 B:ASP102 3.8 24.7 1.0 ND2 B:ASN106 3.8 26.2 1.0 CA B:CA1210 3.8 26.9 1.0 OE1 B:GLU22 3.9 25.8 1.0 N B:ASP105 3.9 25.2 1.0 N B:VAL103 3.9 28.0 1.0 OD2 B:ASP105 4.0 27.0 1.0 CB B:ASP138 4.1 22.5 1.0 CG B:GLU74 4.3 29.8 1.0 CA B:ASP138 4.3 22.7 1.0 CA B:VAL103 4.4 28.4 1.0 OD2 B:ASP138 4.5 23.2 1.0 N B:ASN104 4.5 27.0 1.0 CA B:ASN104 4.5 25.8 1.0 CB B:ASP105 4.5 26.5 1.0 CB B:ASP102 4.5 27.5 1.0 CA B:ASP102 4.7 28.5 1.0 CA B:ASP105 4.7 25.8 1.0 C B:ASN104 4.7 25.8 1.0 CB B:ARG73 4.7 24.5 1.0 NE B:ARG73 4.7 24.2 1.0 C B:ASP102 4.8 28.6 1.0 CG2 B:VAL103 4.8 29.4 1.0 CG B:GLU22 4.8 25.9 1.0 O B:HOH2059 4.9 2.9 1.0 NH2 B:ARG73 5.0 27.9 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1238 b:25.5 occ:1.00 OD1 C:ASN120 2.2 33.1 1.0 OD2 C:ASP157 2.3 25.0 1.0 O C:ASN163 2.3 24.1 1.0 O C:ASN122 2.4 28.4 1.0 OD2 C:ASP215 2.5 26.5 1.0 OD2 C:ASP159 2.5 28.8 1.0 OD1 C:ASP157 2.6 26.7 1.0 CG C:ASP157 2.8 24.9 1.0 CG C:ASN120 3.4 34.1 1.0 CG C:ASP215 3.4 28.6 1.0 CG C:ASP159 3.5 28.7 1.0 C C:ASN122 3.5 29.3 1.0 C C:ASN163 3.5 26.0 1.0 CB C:ASP159 3.7 28.1 1.0 CB C:ASP215 3.9 27.6 1.0 ND2 C:ASN120 4.0 34.6 1.0 CB C:ASP157 4.2 24.8 1.0 CA C:ASN163 4.3 27.5 1.0 N C:ASN122 4.3 32.2 1.0 CB C:ASN163 4.3 28.4 1.0 CA C:ASN122 4.4 31.1 1.0 OD1 C:ASP215 4.4 30.8 1.0 N C:SER123 4.4 29.6 1.0 N C:GLY164 4.5 26.9 1.0 CB C:ASN120 4.6 33.4 1.0 CA C:SER123 4.6 28.1 1.0 CA C:ASN120 4.6 32.2 1.0 CB C:ASN122 4.6 30.5 1.0 OD1 C:ASP159 4.6 30.1 1.0 CA C:GLY164 4.7 27.0 1.0 C C:ASN120 4.8 32.5 1.0 C C:SER123 4.8 27.2 1.0 N C:ASP159 5.0 28.0 1.0 CA C:ASP159 5.0 29.0 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Mouse Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1239 b:33.3 occ:1.00 OD2 C:ASP121 2.2 40.9 1.0 OD1 C:ASP83 2.3 34.7 1.0 OD2 C:ASP85 2.3 28.8 1.0 OE1 C:GLU27 2.3 36.9 1.0 O C:HOH2050 2.4 8.0 1.0 OE2 C:GLU28 2.8 43.4 1.0 CG C:ASP121 3.2 38.5 1.0 CG C:ASP83 3.3 35.6 1.0 CD C:GLU27 3.3 35.5 1.0 CD C:GLU28 3.4 44.5 1.0 CG C:ASP85 3.4 29.9 1.0 OD1 C:ASP121 3.5 36.4 1.0 OE2 C:GLU27 3.8 34.0 1.0 CG C:GLU28 3.9 40.3 1.0 CB C:ASP85 4.0 32.1 1.0 OD2 C:ASP83 4.0 37.9 1.0 CB C:ASP83 4.2 34.7 1.0 CA C:CA1240 4.2 27.6 1.0 OE1 C:GLU28 4.2 48.9 1.0 CA C:ASP83 4.3 32.3 1.0 N C:ASP85 4.3 30.2 1.0 ND2 C:ASN122 4.3 32.1 1.0 CG C:GLU27 4.4 34.3 1.0 N C:ARG84 4.5 28.9 1.0 OD1 C:ASP85 4.5 26.2 1.0 O C:HOH2051 4.5 5.1 1.0 CB C:ASP121 4.6 38.5 1.0 C C:ASP83 4.7 30.7 1.0 CA C:ASP85 4.8 32.0 1.0 CB C:GLU27 5.0 33.1 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