Calcium in PDB 4zt1: Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation

The structure of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation, PDB code: 4zt1 was solved by V.Nardone, A.P.Lucarelli, A.Dalle Vedove, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.65 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.446, 76.417, 73.020, 90.00, 109.98, 90.00
R / Rfree (%)	19.3 / 21.9

The binding sites of Calcium atom in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation (pdb code 4zt1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation, PDB code: 4zt1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:30.8 occ:1.00 O A:ASN104 2.2 29.7 1.0 O A:ASN143 2.3 28.0 1.0 OD2 A:ASP136 2.3 29.2 1.0 OD1 A:ASN102 2.4 31.5 1.0 OD2 A:ASP195 2.5 39.7 1.0 OD2 A:ASP134 2.5 31.1 1.0 OD1 A:ASP134 2.5 30.5 1.0 CG A:ASP134 2.8 34.8 1.0 CG A:ASP136 3.4 34.5 1.0 C A:ASN104 3.4 34.1 1.0 CG A:ASP195 3.5 34.5 1.0 C A:ASN143 3.5 28.6 1.0 CG A:ASN102 3.6 34.8 1.0 CB A:ASP136 3.7 32.8 1.0 CB A:ASP195 3.9 37.0 1.0 CA A:ASN104 4.2 36.5 1.0 N A:ASN104 4.2 34.5 1.0 ND2 A:ASN102 4.3 35.0 1.0 CB A:ASP134 4.3 26.9 1.0 CB A:ASN104 4.4 28.9 1.0 N A:ALA144 4.4 26.9 1.0 CA A:ASN143 4.4 25.7 1.0 CA A:ALA144 4.5 31.2 1.0 N A:LYS105 4.5 32.6 1.0 OD1 A:ASP195 4.5 33.2 1.0 OD1 A:ASP136 4.5 31.9 1.0 CB A:ASN143 4.5 30.2 1.0 CA A:LYS105 4.7 32.9 1.0 CA A:ASN102 4.7 29.4 1.0 CB A:ASN102 4.7 30.7 1.0 C A:LYS105 4.8 32.5 1.0 CD1 A:LEU201 4.9 35.2 1.0 N A:ASP136 4.9 35.9 1.0 CD A:PRO106 4.9 37.3 1.0 N A:PRO106 4.9 37.7 1.0 C A:ASN102 4.9 33.6 1.0 CA A:ASP136 4.9 36.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:31.2 occ:1.00 OD1 A:ASP100 2.2 30.5 1.0 OE2 A:GLU69 2.3 29.2 1.0 OE2 A:GLU11 2.3 29.1 1.0 OD1 A:ASP103 2.4 29.8 1.0 OD1 A:ASP136 2.4 31.9 1.0 O A:GLN101 2.4 35.9 1.0 OE1 A:GLU69 2.7 31.9 1.0 CD A:GLU69 2.8 31.4 1.0 CG A:ASP100 3.2 33.7 1.0 CD A:GLU11 3.4 36.1 1.0 CG A:ASP136 3.4 34.5 1.0 CG A:ASP103 3.6 30.7 1.0 C A:GLN101 3.6 31.4 1.0 OE1 A:GLU11 3.8 35.2 1.0 N A:GLN101 3.8 27.9 1.0 OD2 A:ASP100 3.8 31.5 1.0 ND2 A:ASN104 3.9 31.8 1.0 CA A:CA403 4.0 34.2 1.0 OD2 A:ASP103 4.1 34.0 1.0 CB A:ASP136 4.2 32.8 1.0 N A:ASP103 4.2 28.5 1.0 CG A:GLU69 4.2 33.9 1.0 NE A:ARG68 4.3 32.6 1.0 CA A:GLN101 4.3 32.3 1.0 CA A:ASP136 4.3 36.8 1.0 OD2 A:ASP136 4.4 29.2 1.0 CB A:ASP100 4.4 33.3 1.0 CA A:ASP100 4.5 31.2 1.0 C A:ASP100 4.6 37.0 1.0 CB A:ASP103 4.6 28.8 1.0 N A:ASN102 4.7 31.3 1.0 CG A:GLU11 4.7 31.2 1.0 NH2 A:ARG68 4.8 40.7 1.0 CA A:ASP103 4.9 34.0 1.0 CB A:ARG68 4.9 34.6 1.0 CA A:ASN102 4.9 29.4 1.0 O A:HOH664 4.9 33.7 1.0 CB A:GLN101 5.0 30.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:34.2 occ:1.00 OE1 A:GLU69 2.3 31.9 1.0 OD1 A:ASP67 2.3 35.9 1.0 OD2 A:ASP103 2.3 34.0 1.0 O A:HOH589 2.3 30.5 1.0 O A:HOH664 2.4 33.7 1.0 OE1 A:GLU11 2.5 35.2 1.0 CG A:ASP103 3.1 30.7 1.0 OD1 A:ASP103 3.3 29.8 1.0 CG A:ASP67 3.3 42.0 1.0 CD A:GLU11 3.4 36.1 1.0 CD A:GLU69 3.5 31.4 1.0 OE2 A:GLU11 3.7 29.1 1.0 O A:HOH512 4.0 49.1 1.0 CA A:CA402 4.0 31.2 1.0 OD2 A:ASP67 4.0 34.7 1.0 N A:ARG68 4.1 34.1 1.0 CA A:ASP67 4.2 31.4 1.0 N A:GLU69 4.2 33.0 1.0 CB A:ASP67 4.2 33.0 1.0 CB A:GLU69 4.2 31.4 1.0 OD1 A:ASN12 4.3 33.8 1.0 ND2 A:ASN12 4.3 34.2 1.0 O A:HOH598 4.3 43.5 1.0 ND2 A:ASN104 4.3 31.8 1.0 CG A:GLU69 4.3 33.9 1.0 C A:ASP67 4.4 27.8 1.0 OE2 A:GLU69 4.4 29.2 1.0 O A:HOH617 4.4 43.9 1.0 O A:HOH703 4.5 51.4 1.0 CB A:ASP103 4.6 28.8 1.0 CG A:GLU11 4.7 31.2 1.0 CG A:ASN12 4.7 31.2 1.0 CA A:GLU69 4.8 35.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:29.0 occ:1.00 OD1 B:ASN102 2.2 28.8 1.0 O B:ASN104 2.3 29.2 1.0 OD2 B:ASP134 2.3 27.5 1.0 O B:ASN143 2.3 30.1 1.0 OD2 B:ASP136 2.4 28.4 1.0 OD2 B:ASP195 2.5 39.3 1.0 OD1 B:ASP134 2.6 30.5 1.0 CG B:ASP134 2.8 34.9 1.0 CG B:ASN102 3.4 32.5 1.0 CG B:ASP195 3.4 33.0 1.0 CG B:ASP136 3.4 35.9 1.0 C B:ASN104 3.5 30.2 1.0 C B:ASN143 3.5 27.2 1.0 CB B:ASP136 3.8 31.4 1.0 CB B:ASP195 3.9 31.3 1.0 ND2 B:ASN102 4.0 36.4 1.0 N B:ASN104 4.2 28.5 1.0 CA B:ASN104 4.3 26.3 1.0 CB B:ASP134 4.3 26.9 1.0 OD1 B:ASP195 4.4 38.3 1.0 N B:ALA144 4.4 25.9 1.0 CA B:ASN143 4.5 27.9 1.0 CA B:ALA144 4.5 25.3 1.0 CB B:ASN104 4.5 26.6 1.0 N B:LYS105 4.5 27.5 1.0 OD1 B:ASP136 4.6 32.3 1.0 CB B:ASN102 4.6 31.2 1.0 CB B:ASN143 4.6 31.9 1.0 CA B:ASN102 4.7 34.4 1.0 CA B:LYS105 4.7 32.8 1.0 C B:LYS105 4.7 34.0 1.0 CD1 B:LEU201 4.8 38.6 1.0 CD B:PRO106 4.8 37.2 1.0 N B:PRO106 4.8 31.0 1.0 C B:ASN102 4.9 35.3 1.0 N B:ASP136 4.9 33.6 1.0 CA B:ASP136 5.0 29.1 1.0 N B:ASP103 5.0 30.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:29.1 occ:1.00 OD1 B:ASP136 2.2 32.3 1.0 OE2 B:GLU11 2.2 28.2 1.0 OD1 B:ASP100 2.3 30.9 1.0 O B:GLN101 2.3 36.8 1.0 OD1 B:ASP103 2.4 32.7 1.0 OE2 B:GLU69 2.4 29.2 1.0 OE1 B:GLU69 2.8 30.6 1.0 CD B:GLU69 2.9 25.9 1.0 CG B:ASP136 3.3 35.9 1.0 CD B:GLU11 3.4 31.5 1.0 CG B:ASP100 3.4 33.9 1.0 CG B:ASP103 3.5 35.9 1.0 C B:GLN101 3.5 30.1 1.0 OE1 B:GLU11 3.8 31.1 1.0 N B:GLN101 3.8 34.4 1.0 OD2 B:ASP100 3.9 27.4 1.0 ND2 B:ASN104 3.9 29.8 1.0 CA B:CA403 4.0 31.9 1.0 OD2 B:ASP103 4.0 29.0 1.0 N B:ASP103 4.0 30.1 1.0 CB B:ASP136 4.1 31.4 1.0 CA B:ASP136 4.3 29.1 1.0 CA B:GLN101 4.3 31.2 1.0 OD2 B:ASP136 4.3 28.4 1.0 CG B:GLU69 4.4 26.4 1.0 NE B:ARG68 4.4 32.5 1.0 N B:ASN102 4.5 31.6 1.0 CB B:ASP100 4.6 35.7 1.0 CB B:ASP103 4.6 37.5 1.0 CG B:GLU11 4.6 29.8 1.0 CA B:ASP100 4.7 33.2 1.0 CA B:ASN102 4.7 34.4 1.0 C B:ASP100 4.7 33.7 1.0 CB B:ARG68 4.7 31.8 1.0 CA B:ASP103 4.8 31.4 1.0 CB B:GLN101 4.9 35.3 1.0 C B:ASN102 4.9 35.3 1.0 N B:ASN104 5.0 28.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human E-Cadherin (Residues 3-213) in X-Dimer Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:31.9 occ:1.00 OE1 B:GLU69 2.3 30.6 1.0 OD1 B:ASP67 2.3 31.9 1.0 OD2 B:ASP103 2.3 29.0 1.0 O B:HOH607 2.4 27.4 1.0 O B:HOH524 2.4 26.9 1.0 OE1 B:GLU11 2.4 31.1 1.0 CG B:ASP103 3.1 35.9 1.0 OD1 B:ASP103 3.2 32.7 1.0 CG B:ASP67 3.3 32.8 1.0 CD B:GLU11 3.4 31.5 1.0 CD B:GLU69 3.5 25.9 1.0 OE2 B:GLU11 3.7 28.2 1.0 CA B:CA402 4.0 29.1 1.0 OD2 B:ASP67 4.0 34.2 1.0 N B:ARG68 4.1 28.4 1.0 CA B:ASP67 4.1 29.1 1.0 CB B:ASP67 4.2 31.6 1.0 N B:GLU69 4.2 23.2 1.0 ND2 B:ASN104 4.2 29.8 1.0 ND2 B:ASN12 4.2 31.8 1.0 CB B:GLU69 4.3 27.6 1.0 O B:HOH536 4.3 26.1 1.0 OD1 B:ASN12 4.3 31.1 1.0 C B:ASP67 4.4 32.3 1.0 OE2 B:GLU69 4.4 29.2 1.0 CG B:GLU69 4.4 26.4 1.0 O B:HOH585 4.4 39.8 1.0 O B:HOH575 4.5 35.6 1.0 CB B:ASP103 4.6 37.5 1.0 O B:HOH630 4.6 39.9 1.0 CG B:GLU11 4.7 29.8 1.0 CG B:ASN12 4.7 32.4 1.0 CA B:GLU69 4.9 26.4 1.0

V.Nardone, A.P.Lucarelli, A.Dalle Vedove, R.Fanelli, A.Tomassetti, L.Belvisi, M.Civera, E.Parisini. Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with A Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction. J.Med.Chem. V. 59 5089 2016.
ISSN: ISSN 0022-2623
PubMed: 27120112
DOI: 10.1021/ACS.JMEDCHEM.5B01487