Atomistry » Calcium » PDB 4ae2-4aqe » 4aqa
Atomistry »
  Calcium »
    PDB 4ae2-4aqe »
      4aqa »

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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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

Go back to Calcium Binding Sites List in 4aqa
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: Sat Jul 13 22:11:27 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy