Calcium in PDB 3lne: Crystal Structure of E-Cadherin EC12 K14E

The structure of Crystal Structure of E-Cadherin EC12 K14E, PDB code: 3lne 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)	20.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.001, 48.536, 54.486, 90.00, 111.63, 90.00
R / Rfree (%)	17.2 / 21.9

The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC12 K14E (pdb code 3lne). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of E-Cadherin EC12 K14E, PDB code: 3lne:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of E-Cadherin EC12 K14E


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 K14E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.0 occ:1.00 OD1 A:ASP100 2.4 30.4 1.0 O A:GLN101 2.5 29.3 1.0 OE1 A:GLU11 2.5 37.3 1.0 OD1 A:ASP136 2.6 30.8 1.0 OD1 A:ASP103 2.6 41.4 1.0 OE1 A:GLU69 2.6 26.6 1.0 OE2 A:GLU69 2.6 35.8 1.0 CD A:GLU69 3.0 32.3 1.0 CG A:ASP136 3.4 50.0 1.0 CG A:ASP100 3.4 59.3 1.0 CD A:GLU11 3.5 47.4 1.0 CG A:ASP103 3.6 43.7 1.0 C A:GLN101 3.7 47.1 1.0 OE2 A:GLU11 3.7 35.5 1.0 N A:GLN101 3.7 33.0 1.0 OD2 A:ASP100 3.9 40.5 1.0 ND2 A:ASN104 3.9 32.9 1.0 CA A:CA303 4.0 47.3 1.0 CB A:ASP136 4.0 33.5 1.0 OD2 A:ASP103 4.1 42.2 1.0 N A:ASP103 4.2 22.9 1.0 OD2 A:ASP136 4.3 29.3 1.0 CA A:ASP136 4.3 32.1 1.0 CA A:GLN101 4.3 36.1 1.0 NE A:ARG68 4.3 29.1 1.0 CG A:GLU69 4.4 26.3 1.0 CA A:ASP100 4.6 26.9 1.0 CB A:ASP100 4.6 32.5 1.0 C A:ASP100 4.7 30.5 1.0 N A:ASN102 4.8 33.1 1.0 CB A:ASP103 4.8 26.8 1.0 CG A:GLU11 4.8 29.9 1.0 CB A:ARG68 4.9 30.7 1.0 CB A:GLN101 4.9 38.4 1.0 CA A:ASP103 4.9 28.7 1.0 CA A:ASN102 5.0 27.5 1.0 NH2 A:ARG68 5.0 35.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of E-Cadherin EC12 K14E


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 K14E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.9 occ:1.00 O A:ASN104 2.4 26.3 1.0 O A:ASN143 2.4 25.8 1.0 OD2 A:ASP136 2.5 29.3 1.0 OD1 A:ASN102 2.5 31.5 1.0 OD2 A:ASP195 2.6 26.4 1.0 OD1 A:ASP134 2.6 33.2 1.0 OD2 A:ASP134 2.6 30.6 1.0 CG A:ASP134 3.0 42.4 1.0 CG A:ASP195 3.4 29.6 1.0 CG A:ASP136 3.4 50.0 1.0 C A:ASN104 3.6 46.9 1.0 C A:ASN143 3.6 21.5 1.0 CG A:ASN102 3.7 42.3 1.0 CB A:ASP195 3.8 29.7 1.0 CB A:ASP136 3.9 33.5 1.0 N A:ASN104 4.3 32.4 1.0 CA A:ASN104 4.3 25.5 1.0 ND2 A:ASN102 4.4 27.4 1.0 CA A:ASN143 4.4 30.2 1.0 OD1 A:ASP195 4.4 35.4 1.0 CB A:ASP134 4.5 24.3 1.0 CB A:ASN104 4.5 21.4 1.0 OD1 A:ASP136 4.5 30.8 1.0 CB A:ASN143 4.5 32.2 1.0 N A:ALA144 4.5 24.9 1.0 N A:ARG105 4.6 42.8 1.0 CD1 A:LEU201 4.6 25.6 1.0 CA A:ALA144 4.6 33.0 1.0 CA A:ARG105 4.6 38.7 1.0 CD A:PRO106 4.7 34.6 1.0 CA A:ASN102 4.8 27.5 1.0 CB A:ASN102 4.9 33.8 1.0 N A:ASP136 4.9 35.4 1.0 C A:ARG105 4.9 32.9 1.0 N A:PRO106 4.9 39.3 1.0 C A:ASN102 4.9 33.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of E-Cadherin EC12 K14E


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 K14E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:47.3 occ:1.00 OD2 A:ASP103 2.5 42.2 1.0 OE1 A:GLU69 2.6 26.6 1.0 OD2 A:ASP67 2.6 35.9 1.0 O A:HOH269 2.7 41.2 1.0 OE2 A:GLU11 2.7 35.5 1.0 O A:HOH345 2.8 37.7 1.0 CG A:ASP103 3.3 43.7 1.0 OD1 A:ASP103 3.3 41.4 1.0 CG A:ASP67 3.4 50.8 1.0 CD A:GLU11 3.6 47.4 1.0 CD A:GLU69 3.8 32.3 1.0 OE1 A:GLU11 3.9 37.3 1.0 OD1 A:ASP67 3.9 42.2 1.0 CA A:CA301 4.0 34.0 1.0 ND2 A:ASN104 4.1 32.9 1.0 CA A:ASP67 4.2 32.3 1.0 N A:GLU69 4.2 35.2 1.0 N A:ARG68 4.2 30.6 1.0 O A:HOH484 4.2 37.5 1.0 CB A:ASP67 4.3 32.3 1.0 CB A:GLU69 4.3 40.0 1.0 OD1 A:ASN12 4.4 50.4 1.0 C A:ASP67 4.5 31.3 1.0 ND2 A:ASN12 4.5 29.4 1.0 CG A:GLU69 4.5 26.3 1.0 OE2 A:GLU69 4.6 35.8 1.0 CB A:ASP103 4.7 26.8 1.0 O A:HOH388 4.7 43.9 1.0 CG A:GLU11 4.8 29.9 1.0 CA A:GLU69 4.9 30.4 1.0 CG A:ASN12 4.9 33.8 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