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Calcium in PDB 6cv7: Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3

Protein crystallography data

The structure of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3, PDB code: 6cv7 was solved by G.Dionne, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.11 / 1.69
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.444, 114.444, 172.011, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 18.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 (pdb code 6cv7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3, PDB code: 6cv7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6cv7

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Calcium binding site 1 out of 5 in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:26.0
occ:1.00
 OD2 A:ASP121 2.2 31.5 1.0
OD1 A:ASP83 2.3 35.0 1.0
OD2 A:ASP85 2.3 25.7 1.0
OE1 A:GLU27 2.4 27.1 1.0
O A:HOH848 2.4 25.7 1.0
OE2 A:GLU28 2.6 33.7 1.0
CG A:ASP121 3.1 31.1 1.0
CG A:ASP83 3.2 25.6 1.0
CD A:GLU27 3.3 26.2 1.0
OD1 A:ASP121 3.3 29.0 1.0
CG A:ASP85 3.4 26.2 1.0
CD A:GLU28 3.5 47.6 1.0
OE2 A:GLU27 3.6 22.7 1.0
OD2 A:ASP83 3.6 35.7 1.0
CA A:CA402 3.9 25.9 1.0
CB A:ASP85 4.0 27.5 1.0
CG A:GLU28 4.1 42.9 1.0
CB A:ASP83 4.3 28.7 1.0
ND2 A:ASN122 4.3 25.9 1.0
N A:ASP85 4.4 26.1 1.0
O A:HOH510 4.4 28.0 1.0
O A:HOH686 4.4 45.3 1.0
O A:HOH883 4.4 48.6 1.0
OD1 A:ASP85 4.4 29.1 1.0
OE1 A:GLU28 4.4 41.4 1.0
N A:ARG84 4.4 30.0 1.0
CA A:ASP83 4.5 28.2 1.0
CB A:ASP121 4.5 26.9 1.0
CG A:GLU27 4.5 24.4 1.0
CA A:ASP85 4.9 25.6 1.0
C A:ASP83 4.9 25.8 1.0

Calcium binding site 2 out of 5 in 6cv7

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Calcium binding site 2 out of 5 in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:25.9
occ:1.00
 OD1 A:ASP118 2.4 29.5 1.0
OE2 A:GLU27 2.4 22.7 1.0
OD2 A:ASP85 2.4 25.7 1.0
OD1 A:ASP159 2.4 24.8 1.0
O A:ARG119 2.4 26.8 1.0
OD1 A:ASP85 2.4 29.1 1.0
OD1 A:ASP121 2.4 29.0 1.0
CG A:ASP85 2.8 26.2 1.0
CG A:ASP159 3.4 30.3 1.0
CG A:ASP118 3.4 25.3 1.0
CD A:GLU27 3.4 26.2 1.0
CG A:ASP121 3.5 31.1 1.0
C A:ARG119 3.6 26.3 1.0
N A:ARG119 3.8 26.7 1.0
OE1 A:GLU27 3.9 27.1 1.0
OD2 A:ASP118 3.9 28.9 1.0
CA A:CA401 3.9 26.0 1.0
OD2 A:ASP121 4.0 31.5 1.0
CB A:ASP159 4.0 24.1 1.0
ND2 A:ASN122 4.1 25.9 1.0
N A:ASP121 4.1 28.0 1.0
CA A:ARG119 4.3 26.8 1.0
OD2 A:ASP159 4.3 22.6 1.0
CA A:ASP159 4.3 26.8 1.0
CB A:ASP85 4.3 27.5 1.0
O A:HOH551 4.4 35.9 1.0
CB A:ASP118 4.6 26.6 1.0
C A:ASP118 4.6 29.6 1.0
N A:ASN120 4.6 26.5 1.0
CA A:ASP118 4.6 28.0 1.0
CG A:GLU27 4.7 24.4 1.0
CB A:ASP121 4.7 26.9 1.0
CA A:ASN120 4.8 27.5 1.0
CB A:ARG119 4.8 29.0 1.0
CA A:ASP121 4.9 30.5 1.0

Calcium binding site 3 out of 5 in 6cv7

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Calcium binding site 3 out of 5 in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:22.8
occ:1.00
 OD1 A:ASN120 2.4 31.6 1.0
O A:ASN122 2.4 25.0 1.0
OD2 A:ASP159 2.4 22.6 1.0
O A:ASN163 2.5 27.0 1.0
OD2 A:ASP215 2.5 24.4 1.0
OD2 A:ASP157 2.5 22.8 1.0
OD1 A:ASP157 2.6 27.0 1.0
CG A:ASP157 2.8 29.5 1.0
CG A:ASP159 3.4 30.3 1.0
CG A:ASN120 3.4 30.4 1.0
CG A:ASP215 3.4 25.2 1.0
C A:ASN122 3.5 25.2 1.0
C A:ASN163 3.6 25.5 1.0
CB A:ASP159 3.6 24.1 1.0
CB A:ASP215 3.7 22.7 1.0
ND2 A:ASN120 3.8 31.9 1.0
CA A:ASN122 4.3 24.1 1.0
CB A:ASP157 4.3 23.0 1.0
N A:ASN122 4.3 23.6 1.0
CA A:ASN163 4.4 23.0 1.0
CB A:ASN163 4.4 23.0 1.0
N A:SER123 4.4 26.1 1.0
OD1 A:ASP159 4.5 24.8 1.0
OD1 A:ASP215 4.5 24.9 1.0
N A:GLY164 4.5 23.1 1.0
CB A:ASN122 4.5 31.4 1.0
CA A:SER123 4.6 24.0 1.0
CB A:ASN120 4.6 30.7 1.0
CD A:ARG224 4.7 37.1 1.0
CA A:GLY164 4.7 24.5 1.0
CA A:ASN120 4.8 27.5 1.0
N A:ASP159 4.8 24.9 1.0
CA A:ASP159 4.8 26.8 1.0
C A:ASN120 4.9 27.5 1.0

Calcium binding site 4 out of 5 in 6cv7

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Calcium binding site 4 out of 5 in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:25.6
occ:1.00
 OD1 A:ASP289 2.3 21.9 1.0
OE1 A:GLU137 2.3 25.1 1.0
OD1 A:ASP239 2.3 25.8 1.0
OD1 A:ASP236 2.3 29.7 1.0
O A:HOH885 2.4 28.3 1.0
O A:GLY237 2.4 27.1 1.0
CG A:ASP289 3.3 23.3 1.0
CD A:GLU137 3.4 29.5 1.0
CG A:ASP239 3.5 28.0 1.0
CG A:ASP236 3.6 30.3 1.0
C A:GLY237 3.6 25.4 1.0
N A:GLY237 3.7 28.2 1.0
OE2 A:GLU137 3.8 29.2 1.0
OD2 A:ASP289 4.0 25.0 1.0
CB A:ASP289 4.1 26.1 1.0
O A:HOH563 4.1 30.5 1.0
OD2 A:ASP239 4.2 32.8 1.0
N A:ASP239 4.2 24.1 1.0
CA A:GLY237 4.2 24.7 1.0
OD2 A:ASP236 4.3 31.0 1.0
O A:HOH735 4.4 40.0 1.0
C A:ASP236 4.4 28.3 1.0
CA A:ASP236 4.5 28.2 1.0
CB A:TYR201 4.6 26.4 1.0
CG A:GLU137 4.6 31.7 1.0
CA A:ASP289 4.6 27.1 1.0
CD1 A:LEU240 4.6 26.7 1.0
CG A:LEU240 4.6 26.1 1.0
CB A:ASP236 4.7 26.5 1.0
CB A:ASP239 4.7 25.6 1.0
N A:ASP238 4.7 26.4 1.0
O A:HOH728 4.9 29.6 1.0
N A:LEU240 4.9 24.1 1.0
CA A:ASP239 4.9 23.6 1.0
CA A:ASP238 5.0 26.0 1.0

Calcium binding site 5 out of 5 in 6cv7

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Calcium binding site 5 out of 5 in the Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mouse Protocadherin-15 Extracellular Cadherin Domains 1 Through 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:25.1
occ:1.00
 OD2 A:ASP289 2.4 25.0 1.0
O A:LEU240 2.4 24.8 1.0
OE1 A:GLN348 2.4 24.3 1.0
OD1 A:ASP238 2.4 28.9 1.0
O A:HOH507 2.4 27.0 1.0
OD2 A:ASP287 2.5 34.7 1.0
OD1 A:ASP287 2.6 31.3 1.0
CG A:ASP287 2.8 24.4 1.0
CD A:GLN348 3.3 24.9 1.0
CG A:ASP289 3.3 23.3 1.0
CG A:ASP238 3.5 31.6 1.0
C A:LEU240 3.6 26.7 1.0
NE2 A:GLN348 3.6 27.5 1.0
CB A:ASP289 3.7 26.1 1.0
CA A:ASP238 4.1 26.0 1.0
CB A:ASP238 4.2 26.2 1.0
N A:LEU240 4.2 24.1 1.0
OD2 A:ASP238 4.3 31.1 1.0
CB A:ASP287 4.3 29.6 1.0
CA A:LEU240 4.4 23.7 1.0
OD1 A:ASP289 4.4 21.9 1.0
O A:HOH818 4.5 31.0 1.0
N A:ASP289 4.5 29.0 1.0
N A:GLY241 4.5 24.7 1.0
CA A:GLY241 4.5 24.6 1.0
C A:ASP238 4.6 24.2 1.0
CG A:GLN348 4.7 23.6 1.0
CG A:PRO299 4.7 32.2 1.0
CA A:ASP289 4.8 27.1 1.0
N A:ASP239 4.9 24.1 1.0
CB A:LEU240 4.9 23.6 1.0
C A:GLY241 5.0 27.1 1.0

Reference:

G.Dionne, X.Qiu, M.Rapp, X.Liang, B.Zhao, G.Peng, P.S.Katsamba, G.Ahlsen, R.Rubinstein, C.S.Potter, B.Carragher, B.Honig, U.Mueller. Cis-Dimeric Architecture of PCDH15 Critical For Mechanotransduction Neuron 2018.
ISSN: ISSN 0896-6273
Page generated: Wed Jul 9 13:09:20 2025

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