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Calcium in PDB 1edh: E-Cadherin Domains 1 and 2 in Complex with Calcium

Protein crystallography data

The structure of E-Cadherin Domains 1 and 2 in Complex with Calcium, PDB code: 1edh was solved by B.Nagar, M.Overduin, M.Ikura, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.657, 80.802, 72.635, 90.00, 116.65, 90.00
R / Rfree (%) 20.6 / 26.2

Other elements in 1edh:

The structure of E-Cadherin Domains 1 and 2 in Complex with Calcium also contains other interesting chemical elements:

Mercury (Hg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the E-Cadherin Domains 1 and 2 in Complex with Calcium (pdb code 1edh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the E-Cadherin Domains 1 and 2 in Complex with Calcium, PDB code: 1edh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 1 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:17.6
occ:0.99
 OD2 A:ASP195 2.3 19.8 1.0
O A:ASN104 2.3 20.3 1.0
O A:ASN143 2.4 19.5 1.0
OD2 A:ASP136 2.4 19.0 1.0
OD1 A:ASN102 2.4 21.9 1.0
OD2 A:ASP134 2.5 18.1 1.0
OD1 A:ASP134 2.6 17.9 1.0
CG A:ASP134 2.9 18.5 1.0
CG A:ASP195 3.3 18.2 1.0
CG A:ASP136 3.5 22.5 1.0
C A:ASN104 3.6 19.0 1.0
C A:ASN143 3.6 16.8 1.0
CG A:ASN102 3.6 21.9 1.0
CB A:ASP195 3.8 19.9 1.0
CB A:ASP136 3.8 14.0 1.0
OD1 A:ASP195 4.2 16.0 1.0
ND2 A:ASN102 4.3 18.5 1.0
N A:ASN104 4.3 21.0 1.0
CA A:ASN104 4.3 19.6 1.0
CB A:ASP134 4.4 17.5 1.0
CA A:ALA144 4.4 18.8 1.0
N A:ALA144 4.4 16.4 1.0
CB A:ASN104 4.5 20.2 1.0
CA A:ASN143 4.5 16.9 1.0
N A:ARG105 4.6 23.8 1.0
OD1 A:ASP136 4.6 23.4 1.0
CB A:ASN143 4.6 14.7 1.0
CA A:ARG105 4.7 22.2 1.0
CD1 A:LEU201 4.7 19.7 1.0
CB A:ASN102 4.8 20.4 1.0
CA A:ASN102 4.8 20.8 1.0
C A:ARG105 4.8 19.8 1.0
CD A:PRO106 4.9 15.2 1.0
N A:ASP136 4.9 18.9 1.0
N A:PRO106 4.9 17.5 1.0
C A:ASN102 5.0 23.1 1.0

Calcium binding site 2 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 2 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:17.0
occ:1.00
 OD1 A:ASP103 2.2 13.1 1.0
OD1 A:ASP136 2.3 23.4 1.0
OD1 A:ASP100 2.3 21.1 1.0
OE2 A:GLU11 2.4 16.5 1.0
O A:GLN101 2.4 21.1 1.0
OE2 A:GLU69 2.5 20.5 1.0
OE1 A:GLU69 2.7 17.9 1.0
CD A:GLU69 2.9 20.0 1.0
CG A:ASP103 3.3 15.2 1.0
CG A:ASP136 3.4 22.5 1.0
CG A:ASP100 3.4 18.5 1.0
CD A:GLU11 3.5 17.2 1.0
C A:GLN101 3.6 20.1 1.0
N A:GLN101 3.8 20.9 1.0
ND2 A:ASN104 3.8 23.4 1.0
OE1 A:GLU11 3.9 18.9 1.0
CA A:CA303 3.9 16.9 0.9
OD2 A:ASP103 4.0 19.9 1.0
N A:ASP103 4.0 19.9 1.0
OD2 A:ASP100 4.0 16.0 1.0
CB A:ASP136 4.2 14.0 1.0
OD2 A:ASP136 4.3 19.0 1.0
CA A:GLN101 4.3 19.9 1.0
CG A:GLU69 4.4 22.0 1.0
CA A:ASP136 4.4 17.6 1.0
CB A:ASP103 4.5 17.4 1.0
NE A:ARG68 4.6 23.4 1.0
CB A:ASP100 4.6 17.4 1.0
N A:ASN102 4.7 20.6 1.0
CA A:ASP103 4.7 18.7 1.0
CA A:ASP100 4.7 18.3 1.0
C A:ASP100 4.7 20.1 1.0
CG A:GLU11 4.8 14.6 1.0
CB A:GLN101 4.8 20.4 1.0
CA A:ASN102 4.8 20.8 1.0
C A:ASN102 4.9 23.1 1.0
CG A:ASN104 5.0 25.2 1.0
CB A:ARG68 5.0 19.0 1.0

Calcium binding site 3 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 3 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:16.9
occ:0.87
 O A:HOH407 2.2 15.4 1.0
OD2 A:ASP103 2.2 19.9 1.0
OE1 A:GLU69 2.3 17.9 1.0
OE1 A:GLU11 2.3 18.9 1.0
OD1 A:ASP67 2.4 26.8 1.0
O A:HOH313 2.5 14.4 1.0
CG A:ASP103 3.1 15.2 1.0
OD1 A:ASP103 3.2 13.1 1.0
CD A:GLU11 3.3 17.2 1.0
CG A:ASP67 3.4 23.4 1.0
CD A:GLU69 3.5 20.0 1.0
OE2 A:GLU11 3.6 16.5 1.0
CA A:CA302 3.9 17.0 1.0
OD2 A:ASP67 4.1 23.0 1.0
CA A:ASP67 4.2 20.7 1.0
N A:ARG68 4.2 19.4 1.0
ND2 A:ASN104 4.2 23.4 1.0
OD1 A:ASN12 4.3 18.5 1.0
N A:GLU69 4.3 23.7 1.0
CB A:ASP67 4.3 22.3 1.0
CB A:GLU69 4.3 21.1 1.0
OE2 A:GLU69 4.4 20.5 1.0
ND2 A:ASN12 4.4 20.2 1.0
CG A:GLU69 4.4 22.0 1.0
O A:HOH331 4.4 29.2 1.0
CG A:GLU11 4.5 14.6 1.0
C A:ASP67 4.5 20.3 1.0
CB A:ASP103 4.5 17.4 1.0
O A:HOH368 4.5 38.0 1.0
O A:HOH413 4.6 39.3 1.0
CG A:ASN12 4.7 19.5 1.0
CA A:GLU69 4.9 24.9 1.0

Calcium binding site 4 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 4 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:18.2
occ:1.00
 O B:ASN104 2.2 16.0 1.0
O B:ASN143 2.4 16.2 1.0
OD2 B:ASP195 2.4 17.4 1.0
OD2 B:ASP136 2.4 20.2 1.0
OD1 B:ASN102 2.4 19.2 1.0
OD2 B:ASP134 2.4 20.0 1.0
OD1 B:ASP134 2.5 20.9 1.0
CG B:ASP134 2.8 22.1 1.0
CG B:ASP195 3.4 21.4 1.0
C B:ASN104 3.5 21.0 1.0
CG B:ASP136 3.5 22.1 1.0
C B:ASN143 3.6 18.1 1.0
CG B:ASN102 3.6 24.5 1.0
CB B:ASP195 3.8 20.0 1.0
CB B:ASP136 3.9 19.4 1.0
ND2 B:ASN102 4.2 25.0 1.0
N B:ASN104 4.3 19.4 1.0
OD1 B:ASP195 4.3 20.9 1.0
CA B:ASN104 4.3 19.7 1.0
CB B:ASP134 4.3 16.9 1.0
CA B:ARG105 4.4 25.2 1.0
N B:ARG105 4.4 24.1 1.0
CA B:ASN143 4.5 14.3 1.0
N B:ALA144 4.5 16.6 1.0
CA B:ALA144 4.5 20.6 1.0
CB B:ASN104 4.6 18.2 1.0
CB B:ASN143 4.6 13.5 1.0
OD1 B:ASP136 4.6 23.5 1.0
C B:ARG105 4.7 22.5 1.0
CB B:ASN102 4.8 20.0 1.0
CD1 B:LEU201 4.8 19.6 1.0
CD B:PRO106 4.8 18.1 1.0
CA B:ASN102 4.8 20.6 1.0
N B:ASP136 4.8 21.7 1.0
N B:PRO106 4.9 20.3 1.0

Calcium binding site 5 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 5 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:16.4
occ:1.00
 OD1 B:ASP100 2.3 21.6 1.0
OD1 B:ASP136 2.3 23.5 1.0
OE2 B:GLU11 2.3 14.8 1.0
OD1 B:ASP103 2.4 14.2 1.0
O B:GLN101 2.5 15.2 1.0
OE2 B:GLU69 2.5 14.0 1.0
OE1 B:GLU69 2.8 19.4 1.0
CD B:GLU69 3.0 17.6 1.0
CG B:ASP100 3.4 23.7 1.0
CG B:ASP136 3.4 22.1 1.0
CD B:GLU11 3.5 16.3 1.0
CG B:ASP103 3.5 17.1 1.0
C B:GLN101 3.7 20.3 1.0
N B:GLN101 3.8 21.8 1.0
OD2 B:ASP100 3.9 18.6 1.0
ND2 B:ASN104 3.9 16.9 1.0
OE1 B:GLU11 3.9 14.4 1.0
CA B:CA403 4.1 14.3 0.8
OD2 B:ASP103 4.1 17.8 1.0
CB B:ASP136 4.1 19.4 1.0
N B:ASP103 4.1 18.4 1.0
CA B:ASP136 4.3 19.0 1.0
OD2 B:ASP136 4.4 20.2 1.0
NE B:ARG68 4.4 25.4 1.0
CA B:GLN101 4.4 19.1 1.0
CG B:GLU69 4.4 17.6 1.0
CB B:ASP100 4.5 21.1 1.0
CA B:ASP100 4.6 19.6 1.0
N B:ASN102 4.7 19.1 1.0
CB B:ASP103 4.7 15.1 1.0
C B:ASP100 4.7 22.6 1.0
CG B:GLU11 4.7 14.0 1.0
CB B:ARG68 4.9 18.0 1.0
CA B:ASN102 4.9 20.6 1.0
CB B:GLN101 4.9 20.5 1.0
CA B:ASP103 4.9 16.8 1.0
NH2 B:ARG68 5.0 21.1 1.0

Calcium binding site 6 out of 6 in 1edh

Go back to Calcium Binding Sites List in 1edh
Calcium binding site 6 out of 6 in the E-Cadherin Domains 1 and 2 in Complex with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E-Cadherin Domains 1 and 2 in Complex with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:14.3
occ:0.80
 OD1 B:ASP67 2.1 21.6 1.0
O B:HOH457 2.1 19.9 1.0
OE1 B:GLU69 2.2 19.4 1.0
O B:HOH458 2.2 22.0 1.0
OE1 B:GLU11 2.3 14.4 1.0
OD2 B:ASP103 2.5 17.8 1.0
CG B:ASP67 3.2 22.2 1.0
CD B:GLU11 3.3 16.3 1.0
CG B:ASP103 3.3 17.1 1.0
OD1 B:ASP103 3.4 14.2 1.0
CD B:GLU69 3.5 17.6 1.0
OE2 B:GLU11 3.6 14.8 1.0
OD2 B:ASP67 4.0 20.3 1.0
CA B:CA402 4.1 16.4 1.0
O B:HOH459 4.1 25.8 1.0
CB B:ASP67 4.1 19.2 1.0
CA B:ASP67 4.2 18.0 1.0
CB B:GLU69 4.2 16.1 1.0
N B:GLU69 4.2 16.5 1.0
ND2 B:ASN104 4.2 16.9 1.0
N B:ARG68 4.2 18.7 1.0
CG B:GLU69 4.3 17.6 1.0
OE2 B:GLU69 4.3 14.0 1.0
OD1 B:ASN12 4.4 22.1 1.0
O B:HOH407 4.4 30.0 1.0
C B:ASP67 4.4 18.1 1.0
ND2 B:ASN12 4.6 16.8 1.0
CG B:GLU11 4.6 14.0 1.0
O B:HOH425 4.6 40.6 1.0
CB B:ASP103 4.7 15.1 1.0
CA B:GLU69 4.8 16.1 1.0
CG B:ASN12 4.9 16.1 1.0

Reference:

B.Nagar, M.Overduin, M.Ikura, J.M.Rini. Structural Basis of Calcium-Induced E-Cadherin Rigidification and Dimerization. Nature V. 380 360 1996.
ISSN: ISSN 0028-0836
PubMed: 8598933
DOI: 10.1038/380360A0
Page generated: Sat Dec 12 02:54:06 2020

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