Calcium in PDB 3lnf: Crystal Structure of E-Cadherin EC12 K14EW2A

The structure of Crystal Structure of E-Cadherin EC12 K14EW2A, PDB code: 3lnf was solved by X.Jin, O.Harrison, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.64 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.107, 47.383, 69.897, 70.58, 88.13, 75.50
R / Rfree (%)	18.4 / 24.1

The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC12 K14EW2A (pdb code 3lnf). 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 E-Cadherin EC12 K14EW2A, PDB code: 3lnf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:40.5 occ:1.00 OD2 A:ASP103 2.4 40.7 1.0 OE1 A:GLU69 2.6 32.4 1.0 OD2 A:ASP67 2.6 38.9 1.0 OE2 A:GLU11 2.7 41.8 1.0 CG A:ASP103 3.1 39.8 1.0 OD1 A:ASP103 3.2 37.9 1.0 CG A:ASP67 3.2 45.4 1.0 CD A:GLU11 3.6 37.0 1.0 OD1 A:ASP67 3.8 48.1 1.0 CD A:GLU69 3.8 35.8 1.0 OE1 A:GLU11 3.8 37.9 1.0 ND2 A:ASN104 3.9 33.5 1.0 CA A:CA302 3.9 32.8 1.0 CA A:ASP67 4.1 34.1 1.0 CB A:ASP67 4.1 36.6 1.0 ND2 A:ASN12 4.2 35.9 1.0 N A:ARG68 4.3 36.1 1.0 OD1 A:ASN12 4.4 43.3 1.0 CB A:GLU69 4.5 36.4 1.0 C A:ASP67 4.5 35.4 1.0 N A:GLU69 4.5 36.9 1.0 CB A:ASP103 4.6 36.7 1.0 CG A:GLU69 4.6 40.1 1.0 OE2 A:GLU69 4.7 36.1 1.0 CG A:ASN12 4.7 38.5 1.0 CG A:GLU11 4.9 40.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:32.8 occ:1.00 O A:GLN101 2.4 36.2 1.0 OD1 A:ASP103 2.4 37.9 1.0 OE1 A:GLU11 2.6 37.9 1.0 OD1 A:ASP100 2.6 39.7 1.0 OE2 A:GLU69 2.6 36.1 1.0 OE1 A:GLU69 2.6 32.4 1.0 OD1 A:ASP136 2.7 40.2 1.0 CD A:GLU69 2.9 35.8 1.0 CG A:ASP136 3.2 36.5 1.0 CG A:ASP100 3.3 38.0 1.0 C A:GLN101 3.5 41.3 1.0 CG A:ASP103 3.6 39.8 1.0 CD A:GLU11 3.6 37.0 1.0 ND2 A:ASN104 3.6 33.5 1.0 OD2 A:ASP100 3.7 40.5 1.0 N A:GLN101 3.7 37.0 1.0 OD2 A:ASP136 3.8 38.5 1.0 OE2 A:GLU11 3.9 41.8 1.0 CB A:ASP136 3.9 34.7 1.0 CA A:CA301 3.9 40.5 1.0 N A:ASP103 4.0 30.6 1.0 OD2 A:ASP103 4.1 40.7 1.0 CA A:GLN101 4.2 41.0 1.0 CA A:ASP136 4.2 32.4 1.0 CG A:GLU69 4.3 40.1 1.0 CB A:ASP100 4.5 37.1 1.0 CA A:ASP100 4.5 34.9 1.0 C A:ASP100 4.6 34.1 1.0 NE A:ARG68 4.6 37.0 1.0 N A:ASN102 4.6 35.8 1.0 CB A:ASP103 4.7 36.7 1.0 CB A:GLN101 4.7 39.1 1.0 CA A:ASN102 4.7 34.6 1.0 CA A:ASP103 4.7 37.2 1.0 N A:ASN104 4.8 34.8 1.0 CG A:ASN104 4.8 36.5 1.0 CG A:GLU11 4.9 40.9 1.0 C A:ASN102 4.9 30.2 1.0 CB A:ARG68 4.9 34.0 1.0 C A:ASP103 5.0 34.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:35.0 occ:1.00 O A:ASN104 2.3 35.0 1.0 OD1 A:ASN102 2.4 32.8 1.0 O A:ASN143 2.4 31.1 1.0 OD2 A:ASP136 2.5 38.5 1.0 OD1 A:ASP134 2.5 34.9 1.0 OD2 A:ASP195 2.6 35.1 1.0 OD2 A:ASP134 2.6 41.3 1.0 CG A:ASP134 2.9 34.9 1.0 CG A:ASP195 3.3 34.4 1.0 CG A:ASP136 3.3 36.5 1.0 C A:ASN104 3.4 37.0 1.0 CG A:ASN102 3.5 36.4 1.0 C A:ASN143 3.5 33.3 1.0 CB A:ASP136 3.7 34.7 1.0 CB A:ASP195 3.7 30.5 1.0 N A:ASN104 4.0 34.8 1.0 ND2 A:ASN102 4.1 37.7 1.0 CA A:ASN104 4.1 35.7 1.0 OD1 A:ASP195 4.2 33.6 1.0 CA A:ASN143 4.2 34.5 1.0 OD1 A:ASP136 4.3 40.2 1.0 CB A:ASN143 4.3 38.5 1.0 CB A:ASN104 4.3 36.9 1.0 CB A:ASP134 4.4 37.7 1.0 CD A:PRO106 4.4 38.1 1.0 CD1 A:LEU201 4.4 30.4 1.0 N A:ARG105 4.5 40.1 1.0 N A:ALA144 4.6 33.5 1.0 CA A:ARG105 4.6 37.9 1.0 CA A:ASN102 4.6 34.6 1.0 CB A:ASN102 4.6 36.1 1.0 C A:ASN102 4.7 30.2 1.0 N A:ASP136 4.8 31.1 1.0 CA A:ALA144 4.8 38.2 1.0 N A:PRO106 4.8 37.8 1.0 N A:ASP103 4.8 30.6 1.0 C A:ARG105 4.8 33.1 1.0 CA A:ASP136 4.9 32.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:33.1 occ:1.00 OD1 B:ASP100 2.3 32.8 1.0 OE2 B:GLU69 2.4 31.3 1.0 O B:GLN101 2.4 27.8 1.0 OD1 B:ASP103 2.4 30.7 1.0 OE1 B:GLU11 2.6 34.6 1.0 OE1 B:GLU69 2.8 36.2 1.0 OD1 B:ASP136 2.9 35.5 1.0 CD B:GLU69 2.9 31.9 1.0 CG B:ASP136 3.2 30.3 1.0 CG B:ASP100 3.5 32.8 1.0 ND2 B:ASN104 3.5 35.8 1.0 CG B:ASP103 3.5 37.0 1.0 CD B:GLU11 3.6 34.2 1.0 C B:GLN101 3.6 32.0 1.0 CB B:ASP136 3.7 27.4 1.0 OE2 B:GLU11 3.8 35.4 1.0 CA B:ASP136 3.9 29.8 1.0 N B:GLN101 3.9 31.0 1.0 OD2 B:ASP136 3.9 33.9 1.0 CA B:CA305 4.0 39.7 1.0 OD2 B:ASP100 4.0 38.4 1.0 N B:ASP103 4.0 29.8 1.0 OD2 B:ASP103 4.1 37.4 1.0 CG B:GLU69 4.3 28.7 1.0 CA B:GLN101 4.3 33.1 1.0 NE B:ARG68 4.4 35.0 1.0 N B:ASN102 4.6 35.8 1.0 CB B:ASP103 4.6 38.5 1.0 N B:ASP136 4.7 26.7 1.0 CB B:ASP100 4.7 35.8 1.0 CG B:ASN104 4.7 38.3 1.0 CA B:ASN102 4.7 30.5 1.0 CA B:ASP100 4.8 33.2 1.0 CA B:ASP103 4.8 31.0 1.0 N B:ASN104 4.8 30.7 1.0 CB B:ARG68 4.8 28.9 1.0 C B:ASP100 4.8 30.5 1.0 CG B:GLU11 4.9 36.9 1.0 C B:ASN102 4.9 31.9 1.0 CB B:GLN101 4.9 31.1 1.0 CD B:ARG68 5.0 33.8 1.0 C B:ASP136 5.0 34.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:39.7 occ:1.00 OE2 B:GLU11 2.4 35.4 1.0 OD2 B:ASP103 2.4 37.4 1.0 OE1 B:GLU69 2.4 36.2 1.0 OD2 B:ASP67 2.6 38.9 1.0 O B:HOH229 2.6 35.0 1.0 CG B:ASP67 3.2 38.7 1.0 CG B:ASP103 3.2 37.0 1.0 OD1 B:ASP103 3.3 30.7 1.0 CD B:GLU11 3.4 34.2 1.0 CD B:GLU69 3.6 31.9 1.0 OD1 B:ASP67 3.7 40.3 1.0 OE1 B:GLU11 3.8 34.6 1.0 CA B:CA304 4.0 33.1 1.0 CA B:ASP67 4.0 33.0 1.0 OD1 B:ASN12 4.0 44.0 1.0 CB B:ASP67 4.0 33.5 1.0 ND2 B:ASN104 4.1 35.8 1.0 N B:ARG68 4.1 36.6 1.0 N B:GLU69 4.3 32.9 1.0 C B:ASP67 4.4 35.9 1.0 ND2 B:ASN12 4.4 36.5 1.0 OE2 B:GLU69 4.4 31.3 1.0 CB B:GLU69 4.5 29.5 1.0 CG B:GLU69 4.6 28.7 1.0 CG B:ASN12 4.6 34.8 1.0 CB B:ASP103 4.6 38.5 1.0 CG B:GLU11 4.7 36.9 1.0 O B:HOH273 4.8 39.1 1.0 CB B:GLU11 4.9 38.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of E-Cadherin EC12 K14EW2A


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 E-Cadherin EC12 K14EW2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:30.7 occ:1.00 O B:ASN143 2.3 25.0 1.0 O B:ASN104 2.4 32.9 1.0 OD1 B:ASN102 2.4 34.9 1.0 OD1 B:ASP134 2.5 30.6 1.0 OD2 B:ASP195 2.5 31.2 1.0 OD2 B:ASP136 2.5 33.9 1.0 OD2 B:ASP134 2.6 28.7 1.0 CG B:ASP134 2.9 28.5 1.0 CG B:ASP136 3.2 30.3 1.0 CG B:ASP195 3.3 30.1 1.0 C B:ASN104 3.5 30.4 1.0 C B:ASN143 3.5 29.3 1.0 CG B:ASN102 3.6 36.3 1.0 CB B:ASP195 3.7 29.4 1.0 CB B:ASP136 3.8 27.4 1.0 OD1 B:ASP136 4.1 35.5 1.0 N B:ASN104 4.1 30.7 1.0 OD1 B:ASP195 4.2 28.1 1.0 CA B:ASN104 4.2 29.3 1.0 ND2 B:ASN102 4.3 36.4 1.0 CB B:ASP134 4.3 30.2 1.0 CB B:ASN104 4.4 29.6 1.0 CA B:ASN143 4.4 28.0 1.0 N B:ALA144 4.4 31.4 1.0 CA B:ALA144 4.5 32.0 1.0 CB B:ASN143 4.5 30.6 1.0 N B:ARG105 4.5 30.4 1.0 CA B:ARG105 4.6 33.7 1.0 CD1 B:LEU201 4.6 31.6 1.0 CA B:ASN102 4.6 30.5 1.0 CD B:PRO106 4.6 32.5 1.0 CB B:ASN102 4.6 37.2 1.0 N B:ASP136 4.7 26.7 1.0 C B:ASN102 4.8 31.9 1.0 C B:ARG105 4.8 31.1 1.0 N B:ASP103 4.8 29.8 1.0 N B:PRO106 4.8 34.0 1.0 CA B:ASP136 4.9 29.8 1.0

O.J.Harrison, F.Bahna, P.S.Katsamba, X.Jin, J.Brasch, J.Vendome, G.Ahlsen, K.J.Carroll, S.R.Price, B.Honig, L.Shapiro. Two-Step Adhesive Binding By Classical Cadherins. Nat.Struct.Mol.Biol. V. 17 348 2010.
ISSN: ISSN 1545-9993
PubMed: 20190754
DOI: 10.1038/NSMB.1784