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Calcium in PDB 4aqa: Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I

Protein crystallography data

The structure of Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I, PDB code: 4aqa 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) 34.19 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.293, 40.506, 84.629, 90.00, 102.86, 90.00
R / Rfree (%) 17.782 / 22.775

Other elements in 4aqa:

The structure of Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I (pdb code 4aqa). 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I, PDB code: 4aqa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4aqa

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Calcium binding site 1 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1207

b:21.8
occ:1.00
 O A:ARG5 2.3 25.8 1.0
OD2 A:ASP41 2.3 22.5 1.0
OD2 A:ASP87 2.3 24.4 1.0
OD2 A:ASP39 2.4 25.1 1.0
OD1 A:ASN4 2.4 25.6 1.0
OD2 A:ASP37 2.5 21.9 1.0
OD1 A:ASP37 2.7 22.1 1.0
CG A:ASP37 2.9 21.9 1.0
CG A:ASP41 3.4 22.7 1.0
CG A:ASP87 3.4 24.1 1.0
CG A:ASN4 3.4 27.2 1.0
CG A:ASP39 3.4 26.0 1.0
C A:ARG5 3.4 27.7 1.0
CB A:ASP87 3.8 23.4 1.0
CB A:ASP39 3.8 25.5 1.0
ND2 A:ASN4 3.8 27.8 1.0
N A:ARG5 3.9 29.1 1.0
CB A:ASP41 4.0 22.6 1.0
CA A:ARG5 4.3 29.8 1.0
OD1 A:ASP41 4.3 22.9 1.0
O A:HOH2011 4.3 26.3 1.0
O A:HOH2096 4.3 21.6 1.0
N A:LEU6 4.4 27.6 1.0
CB A:ASP37 4.4 21.9 1.0
OD1 A:ASP87 4.5 24.0 1.0
CA A:LEU6 4.5 26.8 1.0
OD1 A:ASP39 4.6 26.6 1.0
N A:ASP39 4.7 26.4 1.0
CB A:ASN4 4.7 28.6 1.0
C A:LEU6 4.7 25.5 1.0
CD A:PRO7 4.7 23.8 1.0
C A:ASN4 4.8 29.7 1.0
CA A:ASP39 4.8 25.9 1.0
N A:PRO7 4.9 24.1 1.0
CB A:ARG5 4.9 31.4 1.0
CA A:ASN4 4.9 29.5 1.0

Calcium binding site 2 out of 7 in 4aqa

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Calcium binding site 2 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1208

b:11.2
occ:1.00
 OD2 A:ASP187 2.3 11.6 1.0
OD2 A:ASP138 2.3 12.6 1.0
OD2 A:ASP136 2.3 11.4 1.0
O A:ASN106 2.4 13.0 1.0
O A:GLY142 2.4 12.5 1.0
OD1 A:ASN104 2.4 13.0 1.0
OD1 A:ASP136 2.6 11.4 1.0
CG A:ASP136 2.7 11.7 1.0
CG A:ASP187 3.3 11.7 1.0
CG A:ASP138 3.4 12.9 1.0
CG A:ASN104 3.5 13.7 1.0
C A:ASN106 3.5 13.4 1.0
C A:GLY142 3.5 12.4 1.0
CB A:ASP138 3.7 12.6 1.0
CB A:ASP187 3.7 11.6 1.0
ND2 A:ASN104 3.9 13.0 1.0
N A:ASN106 4.1 14.2 1.0
CA A:GLY142 4.2 12.6 1.0
CA A:ASN106 4.2 14.1 1.0
CB A:ASP136 4.2 11.6 1.0
OD1 A:ASP187 4.4 11.4 1.0
N A:ALA107 4.5 13.0 1.0
CB A:ASN106 4.5 14.2 1.0
OD1 A:ASP138 4.5 13.3 1.0
N A:GLY143 4.6 12.5 1.0
CA A:ALA107 4.6 12.8 1.0
N A:ASP138 4.7 12.9 1.0
CB A:ASN104 4.8 14.2 1.0
CA A:GLY143 4.8 12.5 1.0
CA A:ASP138 4.8 12.9 1.0
C A:ALA107 4.8 12.4 1.0
CB A:LEU194 5.0 14.1 1.0

Calcium binding site 3 out of 7 in 4aqa

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Calcium binding site 3 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1209

b:23.3
occ:1.00
 O A:HOH2144 2.3 15.7 1.0
OE1 A:GLU22 2.4 19.6 1.0
OD2 A:ASP105 2.4 17.5 1.0
OE1 A:GLU74 2.4 21.7 1.0
O A:HOH2058 2.4 17.4 1.0
OD1 A:ASP72 2.6 27.5 1.0
OD1 A:ASP105 2.7 16.1 1.0
CG A:ASP105 2.9 16.5 1.0
CD A:GLU22 3.3 19.5 1.0
CG A:ASP72 3.5 27.7 1.0
OE2 A:GLU22 3.6 19.6 1.0
CD A:GLU74 3.6 23.1 1.0
CA A:CA1210 3.8 19.8 1.0
OD2 A:ASP72 4.1 28.8 1.0
ND2 A:ASN106 4.2 14.4 1.0
N A:ARG73 4.2 23.2 1.0
CA A:ASP72 4.2 25.3 1.0
CB A:ASP72 4.3 26.6 1.0
CB A:ASP105 4.4 16.2 1.0
O A:HOH2056 4.4 21.7 1.0
N A:GLU74 4.4 24.4 1.0
O A:HOH2055 4.4 27.1 1.0
CG A:GLU22 4.5 19.3 1.0
CG A:GLU74 4.5 24.3 1.0
OE2 A:GLU74 4.5 22.1 1.0
O A:HOH2145 4.5 25.2 1.0
CB A:GLU74 4.5 25.3 1.0
O A:HOH2173 4.6 30.4 1.0
C A:ASP72 4.6 24.4 1.0
O A:HOH2172 4.7 23.7 1.0

Calcium binding site 4 out of 7 in 4aqa

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Calcium binding site 4 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1210

b:19.8
occ:1.00
 OE2 A:GLU22 2.3 19.6 1.0
O A:VAL103 2.4 15.1 1.0
OD1 A:ASP138 2.4 13.3 1.0
OD1 A:ASP105 2.4 16.1 1.0
OE2 A:GLU74 2.6 22.1 1.0
OE1 A:GLU74 2.7 21.7 1.0
CL A:CL1212 2.8 18.3 1.0
CD A:GLU74 3.0 23.1 1.0
CD A:GLU22 3.4 19.5 1.0
CG A:ASP105 3.5 16.5 1.0
CG A:ASP138 3.5 12.9 1.0
C A:VAL103 3.6 15.3 1.0
OE1 A:GLU22 3.8 19.6 1.0
CA A:CA1209 3.8 23.3 1.0
N A:ASP105 3.8 15.2 1.0
N A:VAL103 4.0 16.3 1.0
CB A:ASP138 4.1 12.6 1.0
OD2 A:ASP105 4.1 17.5 1.0
ND2 A:ASN106 4.1 14.4 1.0
CA A:ASP138 4.3 12.9 1.0
CG A:GLU74 4.4 24.3 1.0
CA A:VAL103 4.5 15.8 1.0
N A:ASN104 4.5 15.0 1.0
NE A:ARG73 4.5 22.1 1.0
CA A:ASN104 4.5 14.6 1.0
OD2 A:ASP138 4.5 12.6 1.0
CB A:ASP105 4.5 16.2 1.0
C A:ASN104 4.6 15.2 1.0
CA A:ASP105 4.6 15.5 1.0
CG A:GLU22 4.7 19.3 1.0
CG2 A:VAL103 4.8 16.1 1.0
CA A:GLY102 4.8 16.4 1.0
C A:GLY102 4.9 16.4 1.0
O A:HOH2144 4.9 15.7 1.0
CB A:ARG73 5.0 22.2 1.0

Calcium binding site 5 out of 7 in 4aqa

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Calcium binding site 5 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1237

b:18.1
occ:1.00
 OD1 B:ASP159 2.3 20.2 1.0
OE2 B:GLU27 2.3 19.8 1.0
OD1 B:ASP121 2.4 21.6 1.0
OD1 B:ASP118 2.4 20.6 1.0
O B:ARG119 2.5 20.7 1.0
OD2 B:ASP85 2.5 22.8 1.0
OD1 B:ASP85 2.5 22.1 1.0
CG B:ASP85 2.8 22.6 1.0
CG B:ASP159 3.3 20.2 1.0
CD B:GLU27 3.4 20.5 1.0
CG B:ASP118 3.5 20.5 1.0
CG B:ASP121 3.5 22.7 1.0
C B:ARG119 3.6 21.9 1.0
N B:ARG119 3.8 21.7 1.0
OE1 B:GLU27 3.8 20.1 1.0
CB B:ASP159 3.9 20.9 1.0
OD2 B:ASP118 4.0 21.1 1.0
OD2 B:ASP121 4.0 23.6 1.0
CA B:CA1238 4.0 20.8 1.0
ND2 B:ASN122 4.0 19.5 1.0
OD2 B:ASP159 4.2 20.4 1.0
CA B:ASP159 4.2 21.0 1.0
N B:ASP121 4.2 21.7 1.0
CA B:ARG119 4.3 23.0 1.0
CB B:ASP85 4.3 23.6 1.0
O B:HOH2146 4.5 19.1 1.0
CB B:ASP118 4.6 20.3 1.0
CA B:ASP118 4.6 20.2 1.0
C B:ASP118 4.6 20.9 1.0
CG B:GLU27 4.7 20.5 1.0
N B:ASN120 4.7 21.5 1.0
CB B:ARG119 4.7 25.8 1.0
CB B:ASP121 4.8 22.9 1.0
CA B:ASN120 4.9 21.8 1.0
CA B:ASP121 5.0 22.3 1.0
N B:ASP85 5.0 23.3 1.0

Calcium binding site 6 out of 7 in 4aqa

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Calcium binding site 6 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1238

b:20.8
occ:1.00
 OD2 B:ASP85 2.3 22.8 1.0
OD2 B:ASP121 2.3 23.6 1.0
OE1 B:GLU27 2.3 20.1 1.0
OD1 B:ASP83 2.4 22.8 1.0
OE2 B:GLU28 2.4 30.1 1.0
O B:HOH2044 2.5 21.7 1.0
CD B:GLU27 3.3 20.5 1.0
CG B:ASP121 3.3 22.7 1.0
CG B:ASP85 3.3 22.6 1.0
CG B:ASP83 3.4 23.9 1.0
OD1 B:ASP121 3.5 21.6 1.0
CD B:GLU28 3.5 30.8 1.0
OE2 B:GLU27 3.7 19.8 1.0
CG B:GLU28 3.9 29.5 1.0
CB B:ASP85 3.9 23.6 1.0
CA B:CA1237 4.0 18.1 1.0
OD2 B:ASP83 4.1 24.3 1.0
O B:HOH2043 4.2 41.2 1.0
ND2 B:ASN122 4.2 19.5 1.0
N B:ASP85 4.2 23.3 1.0
N B:ARG84 4.3 22.5 1.0
CB B:ASP83 4.3 24.1 1.0
CA B:ASP83 4.3 23.6 1.0
OD1 B:ASP85 4.3 22.1 1.0
O B:HOH2145 4.4 24.5 1.0
CG B:GLU27 4.5 20.5 1.0
OE1 B:GLU28 4.6 34.3 1.0
O B:HOH2174 4.6 39.8 1.0
CB B:ASP121 4.7 22.9 1.0
CA B:ASP85 4.7 24.1 1.0
C B:ASP83 4.7 23.1 1.0
O B:HOH2042 4.9 35.5 1.0

Calcium binding site 7 out of 7 in 4aqa

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Calcium binding site 7 out of 7 in the Crystal Structure of Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G 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 Deafness Associated Mutant Mouse Cadherin-23 EC1-2D124G and Protocadherin-15 EC1-2 Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1239

b:16.8
occ:1.00
 OD1 B:ASN120 2.3 21.7 1.0
O B:ASN122 2.3 18.8 1.0
OD2 B:ASP157 2.4 18.4 1.0
O B:ASN163 2.4 19.0 1.0
OD2 B:ASP215 2.5 18.5 1.0
OD2 B:ASP159 2.5 20.4 1.0
OD1 B:ASP157 2.6 19.0 1.0
CG B:ASP157 2.8 18.6 1.0
CG B:ASP215 3.5 18.3 1.0
CG B:ASN120 3.5 22.0 1.0
C B:ASN122 3.5 18.9 1.0
CG B:ASP159 3.5 20.2 1.0
C B:ASN163 3.5 19.6 1.0
CB B:ASP215 3.8 17.8 1.0
CB B:ASP159 3.8 20.9 1.0
ND2 B:ASN120 4.1 22.1 1.0
CA B:ASN122 4.3 19.6 1.0
N B:ASN122 4.3 20.5 1.0
CB B:ASP157 4.3 18.2 1.0
CA B:ASN163 4.4 20.0 1.0
N B:GLY164 4.4 19.9 1.0
CB B:ASN122 4.5 19.0 1.0
N B:SER123 4.5 18.8 1.0
CA B:GLY164 4.5 20.4 1.0
CB B:ASN163 4.6 20.3 1.0
OD1 B:ASP215 4.6 18.5 1.0
OD1 B:ASP159 4.6 20.2 1.0
CD B:ARG224 4.6 27.9 1.0
CA B:SER123 4.6 18.8 1.0
CB B:ASN120 4.7 22.1 1.0
CA B:ASN120 4.7 21.8 1.0
N B:ASP159 4.9 20.7 1.0
C B:ASN120 4.9 22.1 1.0
CD B:PRO124 4.9 17.7 1.0
C B:SER123 4.9 18.1 1.0

Reference:

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
Page generated: Tue Jul 8 18:37:07 2025

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