Atomistry » Calcium » PDB 6cmw-6d7o » 6cv7
Atomistry »
  Calcium »
    PDB 6cmw-6d7o »
      6cv7 »

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

Go back to Calcium Binding Sites List in 6cv7
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

Go back to Calcium Binding Sites List in 6cv7
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

Go back to Calcium Binding Sites List in 6cv7
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

Go back to Calcium Binding Sites List in 6cv7
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

Go back to Calcium Binding Sites List in 6cv7
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: Mon Jul 15 17:29:25 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy