Calcium in PDB 1ff5: Structure of E-Cadherin Double Domain

The structure of Structure of E-Cadherin Double Domain, PDB code: 1ff5 was solved by O.Pertz, D.Bozic, A.W.Koch, C.Fauser, A.Brancaccio, J.Engel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	122.500, 80.560, 73.440, 90.00, 113.98, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Calcium atom in the Structure of E-Cadherin Double Domain (pdb code 1ff5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of E-Cadherin Double Domain, PDB code: 1ff5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:10.6 occ:1.00 O B:ASN104 2.3 20.3 1.0 OD1 B:ASN102 2.4 29.4 1.0 OD2 B:ASP134 2.4 21.5 1.0 O B:ASN143 2.5 27.2 1.0 OD2 B:ASP195 2.5 20.9 1.0 OD2 B:ASP136 2.7 21.6 1.0 OD1 B:ASP134 2.7 24.0 1.0 CG B:ASP134 2.9 11.9 1.0 C B:ASN104 3.5 17.0 1.0 CG B:ASP195 3.5 14.7 1.0 CG B:ASP136 3.6 10.2 1.0 CG B:ASN102 3.6 22.3 1.0 C B:ASN143 3.7 8.2 1.0 CB B:ASP195 3.9 6.9 1.0 CB B:ASP136 4.0 6.1 1.0 N B:ASN104 4.1 9.8 1.0 CA B:ASN104 4.2 8.9 1.0 CB B:ASN104 4.3 13.1 1.0 CB B:ASP134 4.4 6.9 1.0 ND2 B:ASN102 4.4 13.4 1.0 N B:ARG105 4.5 16.4 1.0 CA B:ASN143 4.5 6.2 1.0 OD1 B:ASP195 4.6 8.7 1.0 N B:ALA144 4.6 6.5 1.0 CA B:ALA144 4.6 4.5 1.0 CA B:ASN102 4.6 23.6 1.0 OD1 B:ASP136 4.7 7.2 1.0 CB B:ASN102 4.7 17.9 1.0 CB B:ASN143 4.7 7.4 1.0 CA B:ARG105 4.7 9.7 1.0 C B:ASN102 4.8 22.1 1.0 CD1 B:LEU201 4.9 4.5 1.0 C B:ARG105 4.9 5.3 1.0 N B:ASP103 4.9 20.7 1.0

Calcium binding site 2 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:9.4 occ:1.00 O B:GLN101 2.4 31.9 1.0 OE2 B:GLU69 2.4 6.2 1.0 OE2 B:GLU11 2.4 25.1 1.0 OD1 B:ASP136 2.4 7.2 1.0 OD1 B:ASP100 2.5 17.3 1.0 OD1 B:ASP103 2.7 13.8 1.0 CD B:GLU69 3.1 8.9 1.0 OE1 B:GLU69 3.2 4.7 1.0 CG B:ASP100 3.2 12.2 1.0 CD B:GLU11 3.2 16.3 1.0 CG B:ASP136 3.3 10.2 1.0 OE1 B:GLU11 3.4 20.2 1.0 OD2 B:ASP100 3.5 11.3 1.0 C B:GLN101 3.5 25.0 1.0 N B:GLN101 3.6 19.2 1.0 CG B:ASP103 3.7 4.6 1.0 OD2 B:ASP136 4.0 21.6 1.0 CB B:ASP136 4.0 6.1 1.0 ND2 B:ASN104 4.1 24.9 1.0 OD2 B:ASP103 4.1 7.6 1.0 CA B:GLN101 4.2 19.7 1.0 CA B:ASP136 4.4 7.4 1.0 N B:ASP103 4.4 20.7 1.0 NH1 B:ARG68 4.4 13.4 1.0 CB B:ASP100 4.5 8.2 1.0 CG B:GLU69 4.6 4.9 1.0 CA B:ASP100 4.6 4.7 1.0 CB B:GLN101 4.6 4.8 1.0 CG B:GLU11 4.6 4.7 1.0 C B:ASP100 4.6 9.5 1.0 N B:ASN102 4.7 27.9 1.0 O B:HOH1060 4.8 40.9 1.0 CA A:CA1003 4.8 11.4 1.0 CB B:ASP103 4.8 9.1 1.0 CD B:ARG68 4.9 5.3 1.0 CA B:ASN102 5.0 23.6 1.0

Calcium binding site 3 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:11.4 occ:1.00 O B:HOH1060 2.3 40.9 1.0 OD2 B:ASP103 2.5 7.6 1.0 O B:HOH1115 2.5 13.7 1.0 OD1 B:ASP67 2.6 26.3 1.0 OE1 B:GLU11 2.7 20.2 1.0 OE1 B:GLU69 2.8 4.7 1.0 CG B:ASP67 3.1 21.3 1.0 OD1 B:ASN12 3.2 13.0 1.0 CG B:ASP103 3.5 4.6 1.0 OD2 B:ASP67 3.6 20.4 1.0 CD B:GLU11 3.8 16.3 1.0 OD1 B:ASP103 3.9 13.8 1.0 CB B:ASP67 4.0 7.3 1.0 O B:HOH1071 4.0 32.4 1.0 CD B:GLU69 4.1 8.9 1.0 CA B:ASP67 4.2 5.1 1.0 CG B:ASN12 4.2 25.0 1.0 ND2 B:ASN12 4.4 39.1 1.0 CG B:GLU11 4.6 4.7 1.0 OE2 B:GLU11 4.6 25.1 1.0 ND2 B:ASN104 4.6 24.9 1.0 C B:ASP67 4.7 8.1 1.0 N B:ARG68 4.7 11.7 1.0 CA A:CA1002 4.8 9.4 1.0 CB B:ASP103 4.8 9.1 1.0 CB B:GLU69 4.8 4.5 1.0 N B:GLU69 4.8 17.6 1.0 OE2 B:GLU69 4.9 6.2 1.0 CG B:GLU69 5.0 4.9 1.0

Calcium binding site 4 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:22.3 occ:1.00 O A:ASN143 2.3 26.3 1.0 O A:ASN104 2.4 23.1 1.0 OD2 A:ASP136 2.5 8.8 1.0 OD1 A:ASN102 2.5 18.6 1.0 OD2 A:ASP134 2.5 32.7 1.0 OD1 A:ASP134 2.6 31.2 1.0 OD2 A:ASP195 2.6 22.3 1.0 CG A:ASP134 2.9 17.6 1.0 CG A:ASP136 3.4 4.5 1.0 C A:ASN143 3.5 15.9 1.0 C A:ASN104 3.6 20.2 1.0 CG A:ASP195 3.6 13.9 1.0 CG A:ASN102 3.7 15.6 1.0 CB A:ASP136 3.8 5.0 1.0 CB A:ASP195 3.9 4.7 1.0 N A:ASN104 4.2 19.6 1.0 CA A:ASN104 4.2 16.5 1.0 CB A:ASN104 4.3 14.5 1.0 CB A:ASP134 4.3 4.6 1.0 CA A:ASN143 4.4 10.6 1.0 N A:ALA144 4.4 11.5 1.0 OD1 A:ASP136 4.4 19.1 1.0 CA A:ALA144 4.5 11.1 1.0 ND2 A:ASN102 4.5 9.3 1.0 CB A:ASN143 4.6 13.6 1.0 CA A:ASN102 4.6 24.4 1.0 N A:ARG105 4.6 13.8 1.0 OD1 A:ASP195 4.7 19.6 1.0 CB A:ASN102 4.7 21.5 1.0 CD1 A:LEU201 4.7 7.3 1.0 N A:ASP136 4.8 10.9 1.0 C A:ASN102 4.9 23.9 1.0 CA A:ARG105 4.9 6.8 1.0 CA A:ASP136 4.9 5.2 1.0 CB A:ALA144 5.0 16.9 1.0 N A:ASP103 5.0 20.3 1.0 C A:ARG105 5.0 7.7 1.0

Calcium binding site 5 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1005 b:9.5 occ:1.00 O A:GLN101 2.3 38.1 1.0 OE2 A:GLU69 2.4 8.0 1.0 OD1 A:ASP136 2.5 19.1 1.0 OD1 A:ASP103 2.5 24.6 1.0 OE2 A:GLU11 2.6 26.7 1.0 OD1 A:ASP100 2.6 17.3 1.0 CD A:GLU69 3.1 18.7 1.0 OE1 A:GLU69 3.1 14.4 1.0 CG A:ASP136 3.3 4.5 1.0 CD A:GLU11 3.3 17.8 1.0 CG A:ASP100 3.4 12.1 1.0 C A:GLN101 3.5 29.9 1.0 OE1 A:GLU11 3.5 20.6 1.0 CG A:ASP103 3.5 17.6 1.0 OD2 A:ASP100 3.6 11.5 1.0 N A:GLN101 3.7 15.1 1.0 ND2 A:ASN104 4.0 21.5 1.0 OD2 A:ASP136 4.0 8.8 1.0 OD2 A:ASP103 4.0 19.4 1.0 CB A:ASP136 4.1 5.0 1.0 CA A:GLN101 4.2 22.6 1.0 N A:ASP103 4.2 20.3 1.0 CA A:ASP136 4.5 5.2 1.0 NH1 A:ARG68 4.5 4.5 1.0 CG A:GLU69 4.5 7.0 1.0 N A:ASN102 4.6 27.2 1.0 CB A:GLN101 4.6 8.1 1.0 CB A:ASP100 4.6 14.8 1.0 CG A:GLU11 4.6 4.5 1.0 CA A:ASP100 4.7 6.7 1.0 C A:ASP100 4.7 5.2 1.0 CB A:ASP103 4.7 12.7 1.0 CA A:ASN102 4.9 24.4 1.0 CA A:ASP103 4.9 15.2 1.0 CB A:ARG68 4.9 5.2 1.0

Calcium binding site 6 out of 6 in the Structure of E-Cadherin Double Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of E-Cadherin Double Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1006 b:27.2 occ:1.00 OD1 A:ASP67 2.6 29.2 1.0 OD2 A:ASP103 2.7 19.4 1.0 OE1 A:GLU11 2.8 20.6 1.0 CG A:ASP67 3.0 24.2 1.0 OD1 A:ASN12 3.0 13.5 1.0 OE1 A:GLU69 3.1 14.4 1.0 OD2 A:ASP67 3.5 23.4 1.0 CB A:ASP67 3.7 5.6 1.0 CG A:ASP103 3.7 17.6 1.0 CG A:ASN12 3.9 23.9 1.0 CD A:GLU11 3.9 17.8 1.0 CA A:ASP67 4.0 4.5 1.0 OD1 A:ASP103 4.1 24.6 1.0 ND2 A:ASN12 4.1 40.5 1.0 CD A:GLU69 4.3 18.7 1.0 C A:ASP67 4.6 10.7 1.0 N A:ARG68 4.6 9.3 1.0 CG A:GLU11 4.7 4.5 1.0 OE2 A:GLU11 4.8 26.7 1.0 O A:LEU66 4.9 11.4 1.0 ND2 A:ASN104 4.9 21.5 1.0 CB A:ASP103 5.0 12.7 1.0 N A:GLU69 5.0 13.2 1.0

O.Pertz, D.Bozic, A.W.Koch, C.Fauser, A.Brancaccio, J.Engel. A New Crystal Structure, CA2+ Dependence and Mutational Analysis Reveal Molecular Details of E-Cadherin Homoassociation. Embo J. V. 18 1738 1999.
ISSN: ISSN 0261-4189
PubMed: 10202138
DOI: 10.1093/EMBOJ/18.7.1738