Calcium in PDB 2qvi: Crystal Structure of N-Cadherin Domains EC12

The structure of Crystal Structure of N-Cadherin Domains EC12, PDB code: 2qvi was solved by L.S.Shapiro, K.J.Carroll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 3.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.657, 86.902, 46.708, 90.00, 97.73, 90.00
R / Rfree (%)	25.4 / 29.9

The binding sites of Calcium atom in the Crystal Structure of N-Cadherin Domains EC12 (pdb code 2qvi). 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 N-Cadherin Domains EC12, PDB code: 2qvi:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of N-Cadherin Domains EC12


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 N-Cadherin Domains EC12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:22.5 occ:1.00 OD1 A:ASN102 2.6 34.7 1.0 O A:ASN104 2.7 45.3 1.0 OD1 A:ASP134 2.8 38.1 1.0 OD2 A:ASP136 2.8 39.8 1.0 OD2 A:ASP194 2.9 38.6 1.0 O A:ASN142 3.0 41.6 1.0 OD2 A:ASP134 3.1 37.6 1.0 CG A:ASN102 3.2 37.0 1.0 ND2 A:ASN102 3.2 37.0 1.0 CG A:ASP134 3.3 38.1 1.0 CG A:ASP194 3.3 38.5 1.0 CG A:ASP136 3.6 38.9 1.0 CD1 A:LEU203 3.6 44.7 1.0 OD1 A:ASP194 3.7 38.7 1.0 C A:ASN104 3.7 45.1 1.0 CB A:ASP194 4.0 38.9 1.0 C A:ASN142 4.1 41.5 1.0 CB A:ASP136 4.2 38.5 1.0 OD1 A:ASP136 4.3 36.9 1.0 CG A:LEU203 4.4 45.8 1.0 N A:ASN104 4.4 43.0 1.0 CB A:ASN102 4.5 37.8 1.0 CA A:ASN104 4.5 43.8 1.0 N A:ARG105 4.6 46.5 1.0 CG A:PRO106 4.6 51.1 1.0 CB A:LEU203 4.7 46.7 1.0 CA A:ASN142 4.7 42.3 1.0 CA A:ARG105 4.7 47.9 1.0 CA A:ASN102 4.7 38.3 1.0 CB A:ASP134 4.7 38.2 1.0 C A:ARG105 4.8 49.2 1.0 CB A:ASN104 4.8 43.1 1.0 CD A:PRO106 4.8 51.3 1.0 C A:ASN102 4.9 38.9 1.0 N A:PRO106 5.0 50.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of N-Cadherin Domains EC12


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 N-Cadherin Domains EC12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.8 occ:1.00 OD1 A:ASP103 2.6 48.2 1.0 O A:MET101 2.6 40.1 1.0 OE1 A:GLU69 2.8 20.3 1.0 OD1 A:ASP136 2.8 36.9 1.0 OE2 A:GLU69 2.8 26.1 1.0 OD1 A:ASP100 2.9 37.6 1.0 CD A:GLU69 3.0 25.8 1.0 OE2 A:GLU11 3.1 36.0 1.0 OE1 A:GLU11 3.6 37.9 1.0 CG A:ASP136 3.6 38.9 1.0 CD A:GLU11 3.6 35.2 1.0 CG A:ASP100 3.8 36.9 1.0 C A:MET101 3.8 39.7 1.0 CG A:ASP103 3.8 46.9 1.0 N A:MET101 3.9 36.6 1.0 CA A:ASP136 4.0 39.3 1.0 CB A:ASP136 4.1 38.5 1.0 OD2 A:ASP100 4.2 37.5 1.0 N A:ASP103 4.3 40.2 1.0 CG A:GLU69 4.3 24.8 1.0 OD2 A:ASP103 4.4 47.1 1.0 CA A:MET101 4.5 38.5 1.0 OD2 A:ASP136 4.5 39.8 1.0 OD1 A:ASN104 4.5 45.0 1.0 CA A:CA303 4.5 34.4 1.0 CA A:ASP100 4.8 34.0 1.0 NE A:ARG68 4.8 33.5 1.0 N A:ASP136 4.8 38.6 1.0 N A:ASN102 4.9 39.0 1.0 C A:ASP100 4.9 34.8 1.0 CB A:ASP100 4.9 34.9 1.0 CB A:MET101 4.9 38.6 1.0 CG A:GLU11 4.9 32.1 1.0 CB A:ASP103 5.0 44.4 1.0 CA A:ASN102 5.0 38.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of N-Cadherin Domains EC12


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 N-Cadherin Domains EC12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:34.4 occ:1.00 OD1 A:ASP67 2.6 31.7 1.0 OE1 A:GLU69 2.8 20.3 1.0 OD2 A:ASP103 2.8 47.1 1.0 OD1 A:ASN104 3.1 45.0 1.0 O A:HOH320 3.3 32.1 1.0 OE1 A:GLU11 3.4 37.9 1.0 CG A:ASP103 3.5 46.9 1.0 CG A:ASP67 3.5 31.4 1.0 OD1 A:ASP103 3.6 48.2 1.0 CD A:GLU69 3.8 25.8 1.0 O A:HOH390 4.0 34.6 1.0 OD2 A:ASP67 4.0 34.5 1.0 CG A:GLU69 4.0 24.8 1.0 CB A:GLU69 4.2 25.0 1.0 O A:ASP103 4.2 42.5 1.0 CG A:ASN104 4.2 43.6 1.0 CA A:CA302 4.5 25.8 1.0 CD A:GLU11 4.6 35.2 1.0 CB A:ASP67 4.6 30.0 1.0 CB A:ASP103 4.7 44.4 1.0 ND2 A:ASN104 4.8 42.2 1.0 OE2 A:GLU69 4.9 26.1 1.0 C A:ASP103 4.9 42.4 1.0

L.S.Shapiro, K.J.Carroll, B.Honig. Biophysical Characterization of N-Cadherin and E-Cadherin Homophilic and Heterophilic Interactions To Be Published.