Calcium in PDB 3lng: Crystal Structure of E-Cadherin EC12 Aa Extension

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

Resolution Low / High (Å)	50.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.536, 80.108, 72.691, 90.00, 118.76, 90.00
R / Rfree (%)	21.8 / 26.3

The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC12 Aa Extension (pdb code 3lng). 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 Aa Extension, PDB code: 3lng:
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 Aa Extension


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:28.4 occ:0.99 O A:ASN104 2.3 36.2 1.0 OD2 A:ASP136 2.4 34.9 1.0 OD1 A:ASN102 2.4 35.6 1.0 OD2 A:ASP195 2.4 38.0 1.0 O A:ASN143 2.4 36.2 1.0 OD2 A:ASP134 2.4 33.4 1.0 OD1 A:ASP134 2.5 34.2 1.0 CG A:ASP134 2.8 33.0 1.0 CG A:ASP136 3.4 34.0 1.0 C A:ASN104 3.5 36.4 1.0 CG A:ASP195 3.5 37.7 1.0 CG A:ASN102 3.6 36.3 1.0 C A:ASN143 3.6 36.1 1.0 CB A:ASP136 3.9 34.2 1.0 CB A:ASP195 4.0 38.0 1.0 CA A:ASN104 4.3 36.2 1.0 N A:ASN104 4.3 36.0 1.0 ND2 A:ASN102 4.3 38.4 1.0 CB A:ASP134 4.4 32.3 1.0 CB A:ASN104 4.4 36.3 1.0 OD1 A:ASP195 4.5 34.7 1.0 N A:ARG105 4.5 36.7 1.0 OD1 A:ASP136 4.5 35.3 1.0 N A:ALA144 4.5 35.4 1.0 CA A:ALA144 4.5 35.1 1.0 CA A:ASN143 4.6 37.0 1.0 CB A:ASN143 4.6 37.0 1.0 CA A:ARG105 4.7 36.9 1.0 C A:ARG105 4.7 36.6 1.0 CA A:ASN102 4.7 36.0 1.0 CD A:PRO106 4.7 36.4 1.0 CB A:ASN102 4.7 36.1 1.0 N A:PRO106 4.8 36.6 1.0 CD1 A:LEU201 4.8 38.7 1.0 N A:ASP136 4.9 33.7 1.0 C A:ASN102 5.0 35.8 1.0

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


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:33.9 occ:1.00 OE2 A:GLU69 2.0 39.8 1.0 OD1 A:ASP100 2.2 34.2 1.0 O A:GLN101 2.2 35.8 1.0 OD1 A:ASP103 2.3 33.4 1.0 OE2 A:GLU11 2.3 37.2 1.0 OD1 A:ASP136 2.4 35.3 1.0 CD A:GLU69 2.9 38.5 1.0 OE1 A:GLU69 3.1 39.4 1.0 CG A:ASP100 3.3 34.1 1.0 C A:GLN101 3.4 35.7 1.0 CG A:ASP103 3.4 34.1 1.0 CG A:ASP136 3.4 34.0 1.0 CD A:GLU11 3.4 37.4 1.0 N A:GLN101 3.6 34.6 1.0 ND2 A:ASN104 3.7 38.8 1.0 OE1 A:GLU11 3.8 37.3 1.0 OD2 A:ASP100 3.9 34.3 1.0 N A:ASP103 4.0 35.5 1.0 CA A:CA303 4.0 31.8 0.9 OD2 A:ASP103 4.1 33.0 1.0 CA A:GLN101 4.1 35.3 1.0 CB A:ASP136 4.1 34.2 1.0 CG A:GLU69 4.3 37.4 1.0 OD2 A:ASP136 4.3 34.9 1.0 CA A:ASP136 4.4 34.4 1.0 CB A:ASP100 4.5 34.3 1.0 CB A:ASP103 4.5 34.8 1.0 N A:ASN102 4.5 36.3 1.0 C A:ASP100 4.5 34.3 1.0 CA A:ASP100 4.5 34.0 1.0 NE A:ARG68 4.6 36.3 1.0 CB A:GLN101 4.7 35.1 1.0 CA A:ASP103 4.7 35.1 1.0 CG A:GLU11 4.7 35.5 1.0 CA A:ASN102 4.7 36.0 1.0 O A:HOH234 4.8 30.2 1.0 C A:ASN102 4.9 35.8 1.0 CB A:ARG68 4.9 34.5 1.0 CG A:ASN104 4.9 36.9 1.0 N A:ASN104 5.0 36.0 1.0

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


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:31.8 occ:0.87 O A:HOH214 1.7 32.5 1.0 O A:HOH234 1.9 30.2 1.0 OE1 A:GLU69 2.1 39.4 1.0 OD2 A:ASP103 2.4 33.0 1.0 OE1 A:GLU11 2.5 37.3 1.0 OD1 A:ASP67 2.5 33.9 1.0 CG A:ASP103 3.2 34.1 1.0 OD1 A:ASP103 3.2 33.4 1.0 CG A:ASP67 3.3 34.3 1.0 CD A:GLU11 3.4 37.4 1.0 CD A:GLU69 3.4 38.5 1.0 OE2 A:GLU11 3.7 37.2 1.0 OD2 A:ASP67 3.9 35.5 1.0 CA A:CA302 4.0 33.9 1.0 OE2 A:GLU69 4.0 39.8 1.0 CA A:ASP67 4.1 34.3 1.0 N A:ARG68 4.1 34.7 1.0 ND2 A:ASN104 4.1 38.8 1.0 CB A:ASP67 4.1 34.2 1.0 OD1 A:ASN12 4.2 33.5 1.0 N A:GLU69 4.3 36.5 1.0 C A:ASP67 4.3 34.3 1.0 CB A:GLU69 4.4 37.0 1.0 ND2 A:ASN12 4.5 34.0 1.0 CG A:GLU69 4.5 37.4 1.0 CG A:GLU11 4.6 35.5 1.0 CB A:ASP103 4.6 34.8 1.0 CG A:ASN12 4.8 33.6 1.0 CB A:GLU11 5.0 33.9 1.0 CA A:GLU69 5.0 36.9 1.0

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


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:30.4 occ:0.99 O B:ASN143 2.2 32.9 1.0 OD1 B:ASN102 2.2 33.3 1.0 O B:ASN104 2.4 38.4 1.0 OD2 B:ASP195 2.5 39.1 1.0 OD2 B:ASP134 2.5 33.3 1.0 OD2 B:ASP136 2.5 32.9 1.0 OD1 B:ASP134 2.6 34.2 1.0 CG B:ASP134 2.9 34.9 1.0 CG B:ASP195 3.4 40.1 1.0 CG B:ASN102 3.4 34.9 1.0 C B:ASN143 3.4 33.5 1.0 CG B:ASP136 3.5 32.3 1.0 C B:ASN104 3.6 38.5 1.0 CB B:ASP136 3.9 32.0 1.0 CB B:ASP195 3.9 40.8 1.0 ND2 B:ASN102 4.1 36.0 1.0 N B:ASN104 4.3 36.9 1.0 OD1 B:ASP195 4.3 40.1 1.0 CA B:ASN104 4.3 38.0 1.0 CA B:ASN143 4.4 33.6 1.0 N B:ALA144 4.4 33.5 1.0 CB B:ASP134 4.4 34.8 1.0 CA B:ALA144 4.5 34.0 1.0 CB B:ASN143 4.5 33.8 1.0 CD1 B:LEU201 4.5 45.6 1.0 CB B:ASN104 4.6 37.8 1.0 CB B:ASN102 4.6 34.0 1.0 N B:ARG105 4.7 39.5 1.0 OD1 B:ASP136 4.7 34.8 1.0 CA B:ASN102 4.7 34.0 1.0 CD B:PRO106 4.9 40.1 1.0 C B:ARG105 4.9 40.2 1.0 CA B:ARG105 4.9 40.5 1.0 N B:ASP136 4.9 32.3 1.0 C B:ASN102 4.9 34.5 1.0 N B:PRO106 4.9 40.2 1.0

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


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:31.2 occ:1.00 OE2 B:GLU69 2.3 31.1 1.0 OD1 B:ASP100 2.3 36.5 1.0 OD1 B:ASP136 2.4 34.8 1.0 OE2 B:GLU11 2.4 37.8 1.0 OD1 B:ASP103 2.4 36.9 1.0 O B:GLN101 2.4 32.8 1.0 CD B:GLU69 3.0 33.0 1.0 OE1 B:GLU69 3.1 34.5 1.0 CG B:ASP136 3.4 32.3 1.0 CG B:ASP100 3.4 34.6 1.0 CD B:GLU11 3.5 35.6 1.0 CG B:ASP103 3.6 37.4 1.0 C B:GLN101 3.6 33.2 1.0 N B:GLN101 3.8 32.8 1.0 ND2 B:ASN104 3.9 39.5 1.0 OE1 B:GLU11 3.9 34.9 1.0 OD2 B:ASP100 3.9 36.0 1.0 CA B:CA303 4.0 31.9 0.9 CB B:ASP136 4.0 32.0 1.0 N B:ASP103 4.1 35.0 1.0 OD2 B:ASP136 4.2 32.9 1.0 OD2 B:ASP103 4.2 38.8 1.0 CA B:GLN101 4.3 32.8 1.0 CA B:ASP136 4.3 32.0 1.0 CG B:GLU69 4.4 34.6 1.0 NE B:ARG68 4.5 32.8 1.0 CB B:ASP100 4.6 32.7 1.0 CA B:ASP100 4.6 32.6 1.0 CB B:ASP103 4.6 35.5 1.0 N B:ASN102 4.6 33.6 1.0 C B:ASP100 4.7 32.7 1.0 CG B:GLU11 4.7 35.7 1.0 CA B:ASP103 4.8 35.4 1.0 CA B:ASN102 4.8 34.0 1.0 CB B:GLN101 4.9 32.5 1.0 NH2 B:ARG68 4.9 31.7 1.0 C B:ASN102 5.0 34.5 1.0

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


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 Aa Extension within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:31.9 occ:0.87 O B:HOH236 2.0 30.0 1.0 OE1 B:GLU69 2.0 34.5 1.0 OD1 B:ASP67 2.2 41.4 1.0 O B:HOH217 2.2 29.5 1.0 OE1 B:GLU11 2.5 34.9 1.0 OD2 B:ASP103 2.5 38.8 1.0 OD1 B:ASP103 3.2 36.9 1.0 CG B:ASP67 3.2 38.2 1.0 CD B:GLU69 3.2 33.0 1.0 CG B:ASP103 3.3 37.4 1.0 CD B:GLU11 3.4 35.6 1.0 OE2 B:GLU11 3.7 37.8 1.0 OD2 B:ASP67 3.9 37.4 1.0 CA B:CA302 4.0 31.2 1.0 OE2 B:GLU69 4.0 31.1 1.0 N B:GLU69 4.1 36.3 1.0 ND2 B:ASN104 4.1 39.5 1.0 N B:ARG68 4.2 36.3 1.0 CA B:ASP67 4.2 36.9 1.0 CB B:ASP67 4.2 37.1 1.0 CG B:GLU69 4.3 34.6 1.0 CB B:GLU69 4.3 36.1 1.0 C B:ASP67 4.4 36.4 1.0 OD1 B:ASN12 4.4 33.1 1.0 CG B:GLU11 4.7 35.7 1.0 ND2 B:ASN12 4.7 38.6 1.0 CB B:ASP103 4.8 35.5 1.0 CA B:GLU69 4.8 36.2 1.0 O B:HOH218 4.9 35.1 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