Calcium in PDB 4zte: Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor

The structure of Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor, PDB code: 4zte 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)	42.26 / 2.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.579, 76.835, 72.772, 90.00, 111.14, 90.00
R / Rfree (%)	18.5 / 23

The binding sites of Calcium atom in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor (pdb code 4zte). 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 Complex with A Peptidomimetic Inhibitor, PDB code: 4zte:
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 Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:30.8 occ:1.00 O A:ASN104 2.2 32.6 1.0 OD1 A:ASN102 2.3 35.5 1.0 OD1 A:ASP136 2.4 31.3 1.0 OD2 A:ASP195 2.4 34.7 1.0 O A:ASN143 2.4 29.7 1.0 OD2 A:ASP134 2.4 36.0 1.0 OD1 A:ASP134 2.5 32.1 1.0 CG A:ASP134 2.8 34.6 1.0 CG A:ASP136 3.4 31.4 1.0 C A:ASN104 3.4 31.3 1.0 CG A:ASP195 3.4 34.0 1.0 CG A:ASN102 3.5 31.7 1.0 C A:ASN143 3.6 29.8 1.0 CB A:ASP136 3.8 30.1 1.0 CB A:ASP195 4.0 33.4 1.0 ND2 A:ASN102 4.2 29.4 1.0 CA A:ASN104 4.2 38.2 1.0 N A:ASN104 4.2 32.8 1.0 CB A:ASP134 4.3 35.8 1.0 CB A:ASN104 4.4 33.7 1.0 OD1 A:ASP195 4.5 29.3 1.0 N A:LYS105 4.5 30.1 1.0 CA A:ASN143 4.5 29.5 1.0 OD2 A:ASP136 4.5 31.8 1.0 N A:ALA144 4.5 30.0 1.0 CA A:ALA144 4.6 31.2 1.0 CB A:ASN143 4.6 32.5 1.0 CB A:ASN102 4.7 29.2 1.0 CA A:ASN102 4.7 32.0 1.0 CA A:LYS105 4.7 30.4 1.0 C A:LYS105 4.7 29.8 1.0 N A:ASP136 4.8 39.6 1.0 C A:ASN102 4.8 33.8 1.0 CD1 A:LEU201 4.8 33.1 1.0 N A:PRO106 4.9 33.8 1.0 CD A:PRO106 4.9 35.8 1.0 CA A:ASP136 5.0 33.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:29.6 occ:1.00 OD1 A:ASP100 2.3 26.9 1.0 OD1 A:ASP103 2.3 33.1 1.0 OE2 A:GLU11 2.3 36.5 1.0 OE2 A:GLU69 2.3 31.5 1.0 OD2 A:ASP136 2.4 31.8 1.0 O A:GLN101 2.4 34.0 1.0 OE1 A:GLU69 2.8 32.2 1.0 CD A:GLU69 2.9 34.3 1.0 CG A:ASP100 3.3 36.2 1.0 CG A:ASP136 3.3 31.4 1.0 CD A:GLU11 3.4 33.3 1.0 CG A:ASP103 3.4 36.6 1.0 C A:GLN101 3.5 36.2 1.0 OE1 A:GLU11 3.8 30.9 1.0 N A:GLN101 3.8 33.6 1.0 ND2 A:ASN104 3.9 31.3 1.0 OD2 A:ASP100 3.9 32.7 1.0 OD2 A:ASP103 4.0 33.9 1.0 CA A:CA403 4.0 35.9 1.0 N A:ASP103 4.0 32.8 1.0 CB A:ASP136 4.0 30.1 1.0 CA A:ASP136 4.2 33.4 1.0 CA A:GLN101 4.3 32.6 1.0 OD1 A:ASP136 4.3 31.3 1.0 CG A:GLU69 4.3 32.8 1.0 NE A:ARG68 4.3 36.3 1.0 CB A:ASP100 4.5 30.9 1.0 CB A:ASP103 4.5 34.9 1.0 CA A:ASP100 4.6 30.0 1.0 N A:ASN102 4.6 34.5 1.0 C A:ASP100 4.6 36.7 1.0 NH2 A:ARG68 4.7 40.9 1.0 CG A:GLU11 4.7 31.6 1.0 CA A:ASP103 4.7 32.7 1.0 CA A:ASN102 4.8 32.0 1.0 CB A:GLN101 4.9 33.7 1.0 C A:ASN102 5.0 33.8 1.0 N A:ASN104 5.0 32.8 1.0 CB A:ARG68 5.0 31.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:35.9 occ:1.00 OD2 A:ASP103 2.2 33.9 1.0 OE1 A:GLU69 2.2 32.2 1.0 O A:HOH579 2.3 32.2 1.0 O A:HOH610 2.3 35.6 1.0 OE1 A:GLU11 2.4 30.9 1.0 OD1 A:ASP67 2.4 40.4 1.0 CG A:ASP103 3.0 36.6 1.0 OD1 A:ASP103 3.2 33.1 1.0 CG A:ASP67 3.3 43.0 1.0 CD A:GLU11 3.4 33.3 1.0 CD A:GLU69 3.5 34.3 1.0 OE2 A:GLU11 3.7 36.5 1.0 OD2 A:ASP67 3.9 42.2 1.0 CA A:CA402 4.0 29.6 1.0 N A:ARG68 4.2 34.3 1.0 CB A:ASP67 4.2 39.2 1.0 CA A:ASP67 4.2 35.5 1.0 CB A:GLU69 4.2 32.3 1.0 ND2 A:ASN104 4.3 31.3 1.0 N A:GLU69 4.3 31.4 1.0 OE2 A:GLU69 4.3 31.5 1.0 OD1 A:ASN12 4.3 34.0 1.0 CG A:GLU69 4.4 32.8 1.0 ND2 A:ASN12 4.4 34.6 1.0 O A:HOH595 4.4 48.1 1.0 CB A:ASP103 4.4 34.9 1.0 C A:ASP67 4.5 32.0 1.0 CG A:GLU11 4.6 31.6 1.0 CG A:ASN12 4.8 34.3 1.0 CA A:GLU69 4.9 33.2 1.0 CB A:GLU11 4.9 27.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:30.1 occ:1.00 O B:ASN104 2.3 30.7 1.0 OD1 B:ASN102 2.3 30.1 1.0 OD2 B:ASP136 2.3 31.4 1.0 O B:ASN143 2.3 30.9 1.0 OD2 B:ASP134 2.4 30.9 1.0 OD2 B:ASP195 2.4 32.5 1.0 OD1 B:ASP134 2.6 29.2 1.0 CG B:ASP134 2.8 34.9 1.0 CG B:ASP136 3.4 32.3 1.0 CG B:ASP195 3.4 35.0 1.0 CG B:ASN102 3.5 33.9 1.0 C B:ASN104 3.5 37.6 1.0 C B:ASN143 3.6 26.8 1.0 CB B:ASP136 3.8 29.3 1.0 CB B:ASP195 3.9 32.4 1.0 ND2 B:ASN102 4.1 31.7 1.0 N B:ASN104 4.2 27.9 1.0 CA B:ASN104 4.3 28.9 1.0 CB B:ASP134 4.3 25.2 1.0 OD1 B:ASP195 4.4 34.3 1.0 CB B:ASN104 4.5 32.5 1.0 N B:ALA144 4.5 30.3 1.0 CA B:ASN143 4.5 27.8 1.0 N B:LYS105 4.5 33.8 1.0 OD1 B:ASP136 4.5 33.6 1.0 CA B:ALA144 4.5 28.1 1.0 CB B:ASN143 4.6 28.8 1.0 CD1 B:LEU201 4.7 41.7 1.0 CB B:ASN102 4.7 30.2 1.0 CA B:LYS105 4.7 34.0 1.0 C B:LYS105 4.7 33.0 1.0 CA B:ASN102 4.7 29.4 1.0 N B:PRO106 4.8 29.4 1.0 CD B:PRO106 4.9 31.1 1.0 N B:ASP136 4.9 31.9 1.0 C B:ASN102 5.0 30.8 1.0 CA B:ASP136 5.0 30.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:32.1 occ:1.00 OE2 B:GLU11 2.3 30.1 1.0 OD1 B:ASP136 2.3 33.6 1.0 O B:GLN101 2.3 36.4 1.0 OD1 B:ASP103 2.4 33.5 1.0 OD1 B:ASP100 2.4 32.0 1.0 OE2 B:GLU69 2.5 29.9 1.0 OE1 B:GLU69 2.7 36.0 1.0 CD B:GLU69 2.9 30.5 1.0 CG B:ASP103 3.4 34.0 1.0 CD B:GLU11 3.4 31.1 1.0 CG B:ASP136 3.4 32.3 1.0 CG B:ASP100 3.5 37.3 1.0 C B:GLN101 3.5 32.4 1.0 OE1 B:GLU11 3.8 32.3 1.0 OD2 B:ASP103 3.8 28.3 1.0 ND2 B:ASN104 3.8 31.5 1.0 N B:GLN101 3.8 33.0 1.0 CA B:CA403 4.0 34.6 1.0 OD2 B:ASP100 4.0 30.4 1.0 N B:ASP103 4.1 28.3 1.0 CB B:ASP136 4.1 29.3 1.0 CA B:GLN101 4.2 32.4 1.0 CG B:GLU69 4.3 31.8 1.0 CA B:ASP136 4.3 30.9 1.0 OD2 B:ASP136 4.3 31.4 1.0 NE B:ARG68 4.4 39.8 1.0 N B:ASN102 4.6 32.6 1.0 CB B:ASP103 4.6 33.2 1.0 CB B:ASP100 4.6 36.5 1.0 CA B:ASP100 4.7 35.0 1.0 CG B:GLU11 4.7 28.8 1.0 C B:ASP100 4.7 35.0 1.0 CA B:ASN102 4.7 29.4 1.0 CA B:ASP103 4.8 27.7 1.0 CB B:ARG68 4.8 30.7 1.0 CB B:GLN101 4.9 29.5 1.0 C B:ASN102 4.9 30.8 1.0 NH2 B:ARG68 5.0 37.6 1.0 O B:HOH574 5.0 27.5 1.0 N B:ASN104 5.0 27.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human E-Cadherin (Residues 3-213) in Complex with A Peptidomimetic Inhibitor


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 Complex with A Peptidomimetic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:34.6 occ:1.00 OE1 B:GLU69 2.3 36.0 1.0 OD2 B:ASP103 2.3 28.3 1.0 O B:HOH574 2.3 27.5 1.0 O B:HOH511 2.4 22.9 1.0 OD1 B:ASP67 2.4 33.2 1.0 OE1 B:GLU11 2.4 32.3 1.0 CG B:ASP103 3.2 34.0 1.0 CG B:ASP67 3.3 38.5 1.0 OD1 B:ASP103 3.3 33.5 1.0 CD B:GLU11 3.4 31.1 1.0 CD B:GLU69 3.5 30.5 1.0 OE2 B:GLU11 3.7 30.1 1.0 OD2 B:ASP67 3.9 35.4 1.0 CA B:CA402 4.0 32.1 1.0 CB B:ASP67 4.1 31.5 1.0 CA B:ASP67 4.2 28.0 1.0 CB B:GLU69 4.2 31.7 1.0 N B:ARG68 4.2 26.5 1.0 O B:HOH581 4.2 50.9 1.0 N B:GLU69 4.2 26.3 1.0 CG B:GLU69 4.3 31.8 1.0 ND2 B:ASN104 4.3 31.5 1.0 ND2 B:ASN12 4.3 30.9 1.0 OD1 B:ASN12 4.3 30.9 1.0 O B:HOH558 4.4 39.5 1.0 C B:ASP67 4.4 29.5 1.0 OE2 B:GLU69 4.4 29.9 1.0 CB B:ASP103 4.6 33.2 1.0 CG B:GLU11 4.6 28.8 1.0 CG B:ASN12 4.8 31.5 1.0 CA B:GLU69 4.9 30.8 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