Calcium in PDB 3lni: Crystal Structure of E-Cadherin EC12 E89A

The structure of Crystal Structure of E-Cadherin EC12 E89A, PDB code: 3lni 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)	20.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.630, 77.122, 71.675, 90.00, 115.25, 90.00
R / Rfree (%)	16.6 / 22.8

The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC12 E89A (pdb code 3lni). 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 E89A, PDB code: 3lni:
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 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:19.5 occ:1.00 OD2 A:ASP136 2.3 33.0 1.0 OD1 A:ASN102 2.3 33.1 1.0 O A:ASN104 2.3 32.0 1.0 O A:ASN143 2.4 29.7 1.0 OD2 A:ASP195 2.4 30.0 1.0 OD1 A:ASP134 2.4 31.1 1.0 OD2 A:ASP134 2.6 31.0 1.0 CG A:ASP134 2.9 31.9 1.0 CG A:ASP136 3.4 31.6 1.0 CG A:ASP195 3.4 30.9 1.0 CG A:ASN102 3.5 32.1 1.0 C A:ASN104 3.5 31.1 1.0 C A:ASN143 3.6 29.2 1.0 CB A:ASP136 3.8 30.8 1.0 CB A:ASP195 3.9 30.6 1.0 ND2 A:ASN102 4.1 29.2 1.0 N A:ASN104 4.3 28.8 1.0 CA A:ASN104 4.3 29.8 1.0 OD1 A:ASP195 4.4 28.3 1.0 CB A:ASP134 4.4 31.0 1.0 OD1 A:ASP136 4.5 31.8 1.0 CA A:ASN143 4.5 29.0 1.0 N A:ARG105 4.5 31.7 1.0 CB A:ASN104 4.5 29.1 1.0 N A:ALA144 4.5 29.1 1.0 CA A:ALA144 4.5 29.0 1.0 CA A:ARG105 4.5 33.6 1.0 CB A:ASN143 4.6 28.3 1.0 CB A:ASN102 4.6 30.1 1.0 CA A:ASN102 4.7 30.6 1.0 CD A:PRO106 4.7 34.4 1.0 C A:ARG105 4.8 34.1 1.0 CD1 A:LEU201 4.8 31.2 1.0 N A:PRO106 4.8 34.7 1.0 N A:ASP136 4.8 30.8 1.0 C A:ASN102 5.0 30.3 1.0 CA A:ASP136 5.0 30.9 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of E-Cadherin EC12 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:18.8 occ:1.00 OE2 A:GLU69 2.3 27.4 1.0 O A:GLN101 2.3 32.2 1.0 OD1 A:ASP136 2.3 31.8 1.0 OD1 A:ASP100 2.3 28.3 1.0 OE2 A:GLU11 2.4 32.2 1.0 OD1 A:ASP103 2.4 23.8 1.0 OE1 A:GLU69 2.8 30.4 1.0 CD A:GLU69 2.9 29.3 1.0 CG A:ASP136 3.4 31.6 1.0 CG A:ASP100 3.4 29.8 1.0 CD A:GLU11 3.4 32.5 1.0 CG A:ASP103 3.5 25.8 1.0 C A:GLN101 3.5 31.4 1.0 OE1 A:GLU11 3.8 33.1 1.0 N A:GLN101 3.8 30.2 1.0 ND2 A:ASN104 3.9 26.3 1.0 OD2 A:ASP100 3.9 30.7 1.0 CB A:ASP136 4.0 30.8 1.0 OD2 A:ASP103 4.1 26.0 1.0 N A:ASP103 4.1 28.8 1.0 CA A:CA303 4.1 27.9 1.0 CA A:ASP136 4.2 30.9 1.0 CA A:GLN101 4.2 30.8 1.0 OD2 A:ASP136 4.4 33.0 1.0 CG A:GLU69 4.4 28.9 1.0 NE A:ARG68 4.5 32.2 1.0 N A:ASN102 4.6 30.5 1.0 CB A:ASP100 4.6 30.0 1.0 CA A:ASP100 4.6 30.0 1.0 CB A:ASP103 4.7 27.0 1.0 C A:ASP100 4.7 30.3 1.0 CG A:GLU11 4.7 31.6 1.0 CA A:ASN102 4.8 30.6 1.0 CA A:ASP103 4.8 28.2 1.0 CB A:GLN101 4.8 30.0 1.0 NH2 A:ARG68 4.9 32.3 1.0 C A:ASN102 5.0 30.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of E-Cadherin EC12 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:27.9 occ:1.00 OD1 A:ASP67 2.4 33.0 1.0 OE1 A:GLU69 2.4 30.4 1.0 O A:HOH214 2.4 24.5 1.0 OD2 A:ASP103 2.4 26.0 1.0 OE1 A:GLU11 2.5 33.1 1.0 O A:HOH215 2.5 19.8 1.0 CG A:ASP67 3.3 33.1 1.0 CG A:ASP103 3.3 25.8 1.0 OD1 A:ASP103 3.4 23.8 1.0 CD A:GLU11 3.5 32.5 1.0 CD A:GLU69 3.6 29.3 1.0 OE2 A:GLU11 3.8 32.2 1.0 OD2 A:ASP67 3.9 36.0 1.0 CA A:ASP67 4.1 32.0 1.0 OD1 A:ASN12 4.1 33.0 1.0 CA A:CA302 4.1 18.8 1.0 CB A:ASP67 4.1 31.4 1.0 N A:ARG68 4.1 31.2 1.0 O A:HOH220 4.2 27.0 1.0 ND2 A:ASN12 4.3 30.7 1.0 N A:GLU69 4.3 30.5 1.0 ND2 A:ASN104 4.3 26.3 1.0 CB A:GLU69 4.4 29.7 1.0 OE2 A:GLU69 4.4 27.4 1.0 C A:ASP67 4.4 31.9 1.0 O A:HOH270 4.4 36.0 1.0 CG A:GLU69 4.5 28.9 1.0 O A:HOH238 4.6 26.4 1.0 CG A:ASN12 4.6 32.2 1.0 O A:HOH233 4.6 27.3 1.0 CB A:ASP103 4.7 27.0 1.0 CG A:GLU11 4.7 31.6 1.0 CA A:GLU69 4.9 30.1 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of E-Cadherin EC12 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:17.3 occ:1.00 OD1 B:ASN102 2.3 34.4 1.0 O B:ASN104 2.3 31.1 1.0 O B:ASN143 2.4 32.0 1.0 OD2 B:ASP195 2.4 33.4 1.0 OD2 B:ASP134 2.4 33.7 1.0 OD2 B:ASP136 2.5 30.3 1.0 OD1 B:ASP134 2.5 35.1 1.0 CG B:ASP134 2.8 32.1 1.0 CG B:ASP195 3.4 34.2 1.0 CG B:ASP136 3.5 31.7 1.0 CG B:ASN102 3.5 34.7 1.0 C B:ASN104 3.5 30.4 1.0 C B:ASN143 3.6 31.2 1.0 CB B:ASP136 3.8 30.1 1.0 CB B:ASP195 3.8 33.9 1.0 ND2 B:ASN102 4.1 32.3 1.0 N B:ASN104 4.3 30.1 1.0 CA B:ASN104 4.3 30.1 1.0 OD1 B:ASP195 4.4 35.0 1.0 CB B:ASP134 4.4 32.4 1.0 N B:ALA144 4.4 31.4 1.0 CA B:ASN143 4.5 31.1 1.0 CA B:ALA144 4.5 31.5 1.0 N B:ARG105 4.5 30.4 1.0 CB B:ASN143 4.5 31.3 1.0 CB B:ASN104 4.5 29.9 1.0 OD1 B:ASP136 4.6 31.5 1.0 CA B:ARG105 4.6 31.4 1.0 CB B:ASN102 4.7 33.4 1.0 CD1 B:LEU201 4.7 27.4 1.0 C B:ARG105 4.7 31.6 1.0 CD B:PRO106 4.8 31.4 1.0 N B:ASP136 4.8 30.6 1.0 N B:PRO106 4.8 32.2 1.0 CA B:ASN102 4.8 33.0 1.0 CA B:ASP136 4.9 30.9 1.0 C B:ASN102 5.0 32.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of E-Cadherin EC12 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.1 occ:1.00 OD1 B:ASP136 2.3 31.5 1.0 OD1 B:ASP100 2.4 30.1 1.0 OE2 B:GLU11 2.4 33.5 1.0 O B:GLN101 2.4 33.3 1.0 OD1 B:ASP103 2.4 27.7 1.0 OE2 B:GLU69 2.5 34.5 1.0 OE1 B:GLU69 2.6 31.0 1.0 CD B:GLU69 2.9 32.5 1.0 CD B:GLU11 3.4 31.3 1.0 CG B:ASP136 3.4 31.7 1.0 CG B:ASP100 3.5 30.7 1.0 CG B:ASP103 3.6 29.2 1.0 OE1 B:GLU11 3.6 30.4 1.0 C B:GLN101 3.6 32.8 1.0 CA B:CA303 3.9 20.3 1.0 N B:GLN101 4.0 31.9 1.0 ND2 B:ASN104 4.0 29.6 1.0 OD2 B:ASP100 4.0 29.5 1.0 OD2 B:ASP103 4.0 32.9 1.0 CB B:ASP136 4.1 30.1 1.0 N B:ASP103 4.1 31.2 1.0 OD2 B:ASP136 4.3 30.3 1.0 CA B:ASP136 4.3 30.9 1.0 CG B:GLU69 4.4 29.2 1.0 NE B:ARG68 4.4 30.7 1.0 CA B:GLN101 4.4 32.6 1.0 CB B:ASP100 4.6 30.7 1.0 N B:ASN102 4.6 32.7 1.0 CA B:ASP100 4.7 31.2 1.0 CG B:GLU11 4.7 31.1 1.0 CB B:ASP103 4.7 30.1 1.0 CA B:ASN102 4.8 33.0 1.0 C B:ASP100 4.8 31.2 1.0 CA B:ASP103 4.9 30.1 1.0 CB B:ARG68 4.9 28.3 1.0 C B:ASN102 5.0 32.9 1.0 NH2 B:ARG68 5.0 27.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of E-Cadherin EC12 E89A


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 E89A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:20.3 occ:1.00 O B:HOH219 2.4 14.9 1.0 O B:HOH216 2.4 16.0 1.0 OD1 B:ASP67 2.4 29.2 1.0 OE1 B:GLU11 2.4 30.4 1.0 OE1 B:GLU69 2.5 31.0 1.0 OD2 B:ASP103 2.5 32.9 1.0 OD1 B:ASP103 3.2 27.7 1.0 CG B:ASP103 3.2 29.2 1.0 CG B:ASP67 3.4 31.0 1.0 CD B:GLU11 3.4 31.3 1.0 CD B:GLU69 3.7 32.5 1.0 OE2 B:GLU11 3.8 33.5 1.0 CA B:CA302 3.9 19.1 1.0 N B:ARG68 4.1 30.4 1.0 OD2 B:ASP67 4.2 30.9 1.0 CA B:ASP67 4.2 30.8 1.0 N B:GLU69 4.2 28.7 1.0 CB B:ASP67 4.2 29.1 1.0 CB B:GLU69 4.3 28.6 1.0 ND2 B:ASN104 4.3 29.6 1.0 OD1 B:ASN12 4.3 30.4 1.0 O B:HOH236 4.3 13.6 1.0 O B:HOH335 4.4 31.1 1.0 O B:HOH234 4.4 18.4 1.0 ND2 B:ASN12 4.4 31.9 1.0 CG B:GLU69 4.5 29.2 1.0 C B:ASP67 4.5 30.9 1.0 OE2 B:GLU69 4.6 34.5 1.0 O B:HOH338 4.6 35.3 1.0 CB B:ASP103 4.7 30.1 1.0 CG B:GLU11 4.7 31.1 1.0 CG B:ASN12 4.8 32.6 1.0 CA B:GLU69 4.9 28.3 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