Calcium in PDB 2o72: Crystal Structure Analysis of Human E-Cadherin (1-213)

The structure of Crystal Structure Analysis of Human E-Cadherin (1-213), PDB code: 2o72 was solved by E.Parisini, J.-H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.10 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.341, 41.077, 59.542, 90.00, 111.15, 90.00
R / Rfree (%)	19.1 / 23.4

The binding sites of Calcium atom in the Crystal Structure Analysis of Human E-Cadherin (1-213) (pdb code 2o72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure Analysis of Human E-Cadherin (1-213), PDB code: 2o72:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure Analysis of Human E-Cadherin (1-213)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Human E-Cadherin (1-213) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.3 occ:1.00 O A:ASN104 2.2 20.4 1.0 O A:ASN143 2.4 22.2 1.0 OD2 A:ASP195 2.4 21.4 1.0 OD2 A:ASP136 2.4 19.2 1.0 OD1 A:ASN102 2.5 20.2 1.0 OD2 A:ASP134 2.5 20.5 1.0 OD1 A:ASP134 2.5 20.4 1.0 CG A:ASP134 2.8 21.9 1.0 CG A:ASP195 3.3 21.1 1.0 C A:ASN104 3.4 21.4 1.0 CG A:ASP136 3.4 23.9 1.0 C A:ASN143 3.6 22.2 1.0 CG A:ASN102 3.6 22.4 1.0 CB A:ASP195 3.7 21.1 1.0 CB A:ASP136 3.8 23.3 1.0 N A:ASN104 4.2 21.5 1.0 ND2 A:ASN102 4.2 22.6 1.0 CA A:ASN104 4.2 21.6 1.0 OD1 A:ASP195 4.3 22.0 1.0 CB A:ASP134 4.3 20.7 1.0 N A:LYS105 4.4 22.8 1.0 CA A:ASN143 4.5 23.3 1.0 N A:ALA144 4.5 21.9 1.0 CB A:ASN104 4.5 21.4 1.0 OD1 A:ASP136 4.5 20.2 1.0 CD1 A:LEU201 4.6 20.0 1.0 CB A:ASN143 4.6 23.6 1.0 CA A:LYS105 4.6 24.2 1.0 CA A:ALA144 4.6 22.4 1.0 C A:LYS105 4.7 23.2 1.0 N A:PRO106 4.8 23.2 1.0 CD A:PRO106 4.8 22.8 1.0 N A:ASP136 4.8 23.5 1.0 CB A:ASN102 4.8 22.5 1.0 CA A:ASN102 4.8 22.4 1.0 C A:ASN102 4.9 21.7 1.0 N A:ASP103 5.0 21.2 1.0 CA A:ASP136 5.0 24.0 1.0

Calcium binding site 2 out of 5 in the Crystal Structure Analysis of Human E-Cadherin (1-213)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Human E-Cadherin (1-213) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:23.5 occ:1.00 OE2 A:GLU69 2.2 18.2 1.0 OD1 A:ASP103 2.3 22.0 1.0 OD1 A:ASP100 2.3 22.2 1.0 OE2 A:GLU11 2.4 19.4 1.0 O A:GLN101 2.4 22.3 1.0 OD1 A:ASP136 2.4 20.2 1.0 OE1 A:GLU69 2.7 23.5 1.0 CD A:GLU69 2.8 19.0 1.0 CG A:ASP100 3.3 22.0 1.0 CG A:ASP103 3.4 21.5 1.0 CD A:GLU11 3.4 24.2 1.0 CG A:ASP136 3.5 23.9 1.0 C A:GLN101 3.6 23.4 1.0 N A:GLN101 3.8 24.0 1.0 OE1 A:GLU11 3.8 26.0 1.0 OD2 A:ASP100 3.9 21.8 1.0 ND2 A:ASN104 4.0 25.2 1.0 OD2 A:ASP103 4.0 24.2 1.0 CA A:CA403 4.0 25.9 1.0 N A:ASP103 4.1 21.2 1.0 CB A:ASP136 4.1 23.3 1.0 CG A:GLU69 4.3 23.0 1.0 CA A:GLN101 4.3 24.1 1.0 OD2 A:ASP136 4.4 19.2 1.0 CA A:ASP136 4.4 24.0 1.0 NE A:ARG68 4.4 25.9 1.0 CB A:ASP100 4.5 23.4 1.0 CA A:ASP100 4.5 24.3 1.0 CB A:ASP103 4.6 21.3 1.0 N A:ASN102 4.6 22.2 1.0 C A:ASP100 4.6 23.9 1.0 CG A:GLU11 4.7 24.9 1.0 CA A:ASP103 4.8 21.5 1.0 NH2 A:ARG68 4.8 23.8 1.0 CA A:ASN102 4.8 22.4 1.0 C A:ASN102 5.0 21.7 1.0 CB A:ARG68 5.0 23.7 1.0 CB A:GLN101 5.0 24.9 1.0

Calcium binding site 3 out of 5 in the Crystal Structure Analysis of Human E-Cadherin (1-213)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Human E-Cadherin (1-213) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:25.9 occ:1.00 OD1 A:ASP67 2.2 24.2 1.0 OD2 A:ASP103 2.2 24.2 1.0 OE1 A:GLU69 2.3 23.5 1.0 O A:HOH479 2.4 23.6 1.0 O A:HOH428 2.4 26.6 1.0 OE1 A:GLU11 2.4 26.0 1.0 CG A:ASP103 3.1 21.5 1.0 OD1 A:ASP103 3.2 22.0 1.0 CG A:ASP67 3.2 22.6 1.0 CD A:GLU11 3.3 24.2 1.0 CD A:GLU69 3.6 19.0 1.0 OE2 A:GLU11 3.7 19.4 1.0 O A:HOH446 3.9 30.7 1.0 OD2 A:ASP67 4.0 18.5 1.0 CA A:CA402 4.0 23.5 1.0 CA A:ASP67 4.1 23.1 1.0 CB A:ASP67 4.2 23.1 1.0 N A:ARG68 4.2 23.3 1.0 ND2 A:ASN104 4.3 25.2 1.0 N A:GLU69 4.3 24.5 1.0 CB A:GLU69 4.3 24.5 1.0 OE2 A:GLU69 4.3 18.2 1.0 OD1 A:ASN12 4.4 25.1 1.0 ND2 A:ASN12 4.4 27.6 1.0 C A:ASP67 4.5 22.8 1.0 CG A:GLU69 4.5 23.0 1.0 O A:HOH540 4.5 32.0 1.0 CB A:ASP103 4.5 21.3 1.0 CG A:GLU11 4.5 24.9 1.0 CG A:ASN12 4.8 28.1 1.0 CA A:GLU69 4.9 24.5 1.0 CB A:GLU11 4.9 25.6 1.0

Calcium binding site 4 out of 5 in the Crystal Structure Analysis of Human E-Cadherin (1-213)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Human E-Cadherin (1-213) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:33.0 occ:1.00 O A:HOH639 2.4 40.4 1.0 OD1 A:ASP180 2.4 18.1 1.0 O A:HOH624 2.6 40.1 1.0 OE1 A:GLU119 2.8 23.3 1.0 OE2 A:GLU119 3.1 32.4 1.0 CD A:GLU119 3.3 28.5 1.0 CA A:CA405 3.3 92.4 1.0 CG A:ASP180 3.4 21.0 1.0 CG A:GLU182 4.1 27.3 1.0 OD2 A:ASP180 4.1 18.1 1.0 N A:GLU182 4.2 21.1 1.0 N A:ARG181 4.2 20.5 1.0 CA A:ASP180 4.2 20.6 1.0 CB A:ASP180 4.2 20.5 1.0 OE2 A:GLU182 4.2 36.5 1.0 CB A:GLU182 4.3 22.3 1.0 C A:ASP180 4.4 20.0 1.0 CD A:GLU182 4.7 29.6 1.0 CG A:GLU119 4.8 25.2 1.0 CA A:GLU182 4.8 22.8 1.0

Calcium binding site 5 out of 5 in the Crystal Structure Analysis of Human E-Cadherin (1-213)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Human E-Cadherin (1-213) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:92.4 occ:1.00 O A:HOH624 2.7 40.1 1.0 O A:HOH546 2.9 50.6 1.0 OD1 A:ASP213 3.1 38.4 1.0 OE2 A:GLU182 3.1 36.5 1.0 CA A:CA404 3.3 33.0 1.0 NH1 A:ARG181 3.3 42.6 1.0 OE2 A:GLU119 3.5 32.4 1.0 CD A:GLU182 3.7 29.6 1.0 CG A:GLU182 3.8 27.3 1.0 OE1 A:GLU119 4.2 23.3 1.0 CD A:GLU119 4.2 28.5 1.0 CG A:ASP213 4.2 31.9 1.0 O A:HOH565 4.6 43.6 1.0 CZ A:ARG181 4.7 36.1 1.0 OD2 A:ASP213 4.8 40.9 1.0 OE1 A:GLU182 4.9 36.6 1.0 CB A:GLU182 5.0 22.3 1.0

E.Parisini, J.M.G.Higgins, J.-H.Liu, M.B.Brenner, J.-H.Wang. The Crystal Structure of Human E-Cadherin Domains 1 and 2, and Comparison with Other Cadherins in the Context of Adhesion Mechanism J.Mol.Biol. V. 373 401 2007.
ISSN: ISSN 0022-2836
PubMed: 17850815
DOI: 10.1016/J.JMB.2007.08.011