Calcium in PDB 3k5s: Crystal Structure of Chicken T-Cadherin EC1 EC2

The structure of Crystal Structure of Chicken T-Cadherin EC1 EC2, PDB code: 3k5s was solved by L.Shapiro, C.Ciatto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.00 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.804, 79.188, 105.162, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 29.4

The binding sites of Calcium atom in the Crystal Structure of Chicken T-Cadherin EC1 EC2 (pdb code 3k5s). 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 Chicken T-Cadherin EC1 EC2, PDB code: 3k5s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca218 b:11.2 occ:1.00 O A:ASN103 2.4 17.7 1.0 O A:ASN141 2.5 15.5 1.0 OD2 A:ASP197 2.6 21.5 1.0 OD1 A:ASN101 2.6 17.0 1.0 OD2 A:ASP133 2.7 17.7 1.0 OD1 A:ASP133 2.7 18.0 1.0 CG A:ASP133 3.1 18.7 1.0 OD2 A:ASP135 3.1 16.1 1.0 OD1 A:ASP197 3.2 21.7 1.0 CG A:ASP197 3.2 20.4 1.0 C A:ASN141 3.5 15.3 1.0 CG A:ASP135 3.6 16.1 1.0 C A:ASN103 3.6 15.2 1.0 CG A:ASN101 3.7 17.2 1.0 CB A:ASP135 3.9 14.1 1.0 ND2 A:ASN101 4.2 19.1 1.0 N A:ASN103 4.2 14.3 1.0 N A:ALA142 4.3 18.3 1.0 CA A:ASN103 4.3 16.8 1.0 CD A:PRO105 4.3 20.5 1.0 CA A:ASN141 4.4 14.1 1.0 OD1 A:ASP135 4.4 16.6 1.0 CB A:ASP133 4.6 14.1 1.0 CB A:ASN103 4.6 16.5 1.0 N A:ARG104 4.6 14.6 1.0 CB A:ASN141 4.6 15.1 1.0 CA A:ALA142 4.6 15.6 1.0 CB A:ASP197 4.6 18.3 1.0 CA A:ARG104 4.7 18.1 1.0 N A:PRO105 4.7 19.9 1.0 CD1 A:LEU205 4.8 17.2 1.0 CG A:PRO105 4.9 17.8 1.0 C A:ARG104 4.9 19.9 1.0 N A:ASP135 4.9 15.0 1.0 CB A:ASN101 4.9 12.4 1.0 CA A:ASN101 5.0 13.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca219 b:14.3 occ:1.00 OD2 A:ASP99 2.5 16.3 1.0 OE2 A:GLU68 2.6 19.6 1.0 OE1 A:GLU11 2.6 15.4 1.0 O A:GLN100 2.7 14.4 1.0 OD1 A:ASP102 2.8 16.7 1.0 OD1 A:ASP135 2.9 16.6 1.0 CD A:GLU68 3.0 18.8 1.0 OE1 A:GLU68 3.0 15.0 1.0 CG A:ASP135 3.3 16.1 1.0 CG A:ASP102 3.5 17.1 1.0 CD A:GLU11 3.5 16.0 1.0 OD2 A:ASP135 3.6 16.1 1.0 CG A:ASP99 3.7 15.2 1.0 OE2 A:GLU11 3.7 19.3 1.0 OD2 A:ASP102 3.8 18.7 1.0 C A:GLN100 3.8 14.3 1.0 N A:GLN100 3.9 17.2 1.0 ND2 A:ASN103 4.0 17.5 1.0 NE A:ARG67 4.0 14.9 1.0 N A:ASP102 4.0 16.6 1.0 CB A:ASP135 4.1 14.1 1.0 CA A:CA220 4.1 19.6 1.0 OD1 A:ASP99 4.3 15.7 1.0 CG A:GLU68 4.3 21.0 1.0 CA A:ASP135 4.3 16.4 1.0 CA A:GLN100 4.5 17.4 1.0 CB A:ARG67 4.7 14.8 1.0 CB A:ASP102 4.7 16.8 1.0 CA A:ASP102 4.7 15.0 1.0 CA A:ASP99 4.8 14.8 1.0 CD A:ARG67 4.8 14.4 1.0 NH2 A:ARG67 4.8 15.1 1.0 N A:ASN101 4.8 13.8 1.0 CB A:ASP99 4.8 18.1 1.0 C A:ASP99 4.8 16.3 1.0 N A:ASN103 4.9 14.3 1.0 CZ A:ARG67 4.9 14.7 1.0 CG A:GLU11 4.9 18.5 1.0 CA A:ASN101 4.9 13.6 1.0 C A:ASP102 5.0 14.7 1.0 C A:ASN101 5.0 14.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca220 b:19.6 occ:1.00 OD2 A:ASP102 2.5 18.7 1.0 OE2 A:GLU11 2.5 19.3 1.0 OD1 A:ASP66 2.5 17.9 1.0 OE2 A:GLU68 2.9 19.6 1.0 OD1 A:ASP102 3.0 16.7 1.0 CG A:ASP102 3.0 17.1 1.0 CG A:ASP66 3.3 17.2 1.0 CD A:GLU11 3.6 16.0 1.0 CG A:GLU68 3.7 21.0 1.0 CD A:GLU68 3.7 18.8 1.0 OD1 A:ASN12 3.9 25.4 1.0 OD2 A:ASP66 4.0 14.6 1.0 OE1 A:GLU11 4.1 15.4 1.0 N A:ARG67 4.1 16.1 1.0 CA A:CA219 4.1 14.3 1.0 CB A:ASP66 4.2 17.6 1.0 ND2 A:ASN12 4.2 21.4 1.0 CA A:ASP66 4.2 16.1 1.0 CB A:ASP102 4.4 16.8 1.0 CG A:ASN12 4.5 20.2 1.0 N A:GLU68 4.5 15.6 1.0 C A:ASP66 4.5 16.0 1.0 ND2 A:ASN103 4.6 17.5 1.0 CG A:GLU11 4.8 18.5 1.0 OE1 A:GLU68 4.8 15.0 1.0 CB A:GLU68 4.9 14.6 1.0 CB A:GLU11 5.0 14.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca218 b:11.9 occ:1.00 OD2 B:ASP135 2.4 15.4 1.0 O B:ASN103 2.5 18.8 1.0 O B:ASN141 2.6 20.2 1.0 OD2 B:ASP133 2.6 18.7 1.0 OD1 B:ASN101 2.7 18.9 1.0 OD2 B:ASP197 2.7 23.8 1.0 OD1 B:ASP133 3.0 14.0 1.0 CG B:ASP133 3.1 18.0 1.0 OD1 B:ASP197 3.2 23.8 1.0 CG B:ASP197 3.3 23.5 1.0 CG B:ASP135 3.5 18.2 1.0 C B:ASN103 3.7 19.0 1.0 CG B:ASN101 3.7 17.1 1.0 C B:ASN141 3.8 18.0 1.0 CB B:ASP135 4.0 16.3 1.0 ND2 B:ASN101 4.2 17.8 1.0 N B:ASN103 4.4 16.6 1.0 CA B:ASN103 4.4 17.6 1.0 CB B:ASN103 4.5 15.9 1.0 OD1 B:ASP135 4.5 19.6 1.0 CD B:PRO105 4.5 23.4 1.0 CA B:ALA142 4.6 15.7 1.0 CB B:ASP133 4.6 18.6 1.0 CA B:ASN141 4.6 20.1 1.0 N B:ALA142 4.7 19.4 1.0 N B:ARG104 4.7 21.7 1.0 CB B:ASP197 4.7 24.9 1.0 CA B:ARG104 4.9 19.8 1.0 CG B:PRO105 4.9 21.7 1.0 CB B:ASN101 4.9 13.9 1.0 N B:PRO105 4.9 20.9 1.0 CB B:ASN141 5.0 17.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca219 b:13.6 occ:1.00 OE2 B:GLU68 2.4 20.7 1.0 OD1 B:ASP135 2.5 19.6 1.0 O B:GLN100 2.5 17.9 1.0 OE1 B:GLU11 2.5 16.5 1.0 OD2 B:ASP99 2.6 18.6 1.0 OD1 B:ASP102 2.7 19.2 1.0 OE1 B:GLU68 2.9 19.0 1.0 CD B:GLU68 3.0 22.1 1.0 CG B:ASP99 3.3 19.8 1.0 CG B:ASP135 3.5 18.2 1.0 CD B:GLU11 3.6 19.3 1.0 OD1 B:ASP99 3.7 17.1 1.0 C B:GLN100 3.7 14.6 1.0 N B:GLN100 3.7 17.9 1.0 CG B:ASP102 3.8 18.2 1.0 CB B:ASP135 4.0 16.3 1.0 CA B:ASP135 4.0 16.1 1.0 ND2 B:ASN103 4.0 17.7 1.0 OE2 B:GLU11 4.1 24.3 1.0 N B:ASP102 4.2 17.9 1.0 NE B:ARG67 4.3 23.9 1.0 OD2 B:ASP102 4.3 17.6 1.0 CA B:GLN100 4.3 17.4 1.0 CA B:CA220 4.4 24.4 1.0 OD2 B:ASP135 4.4 15.4 1.0 CA B:ASP99 4.4 18.2 1.0 CB B:ASP99 4.5 22.9 1.0 CG B:GLU68 4.5 24.2 1.0 C B:ASP99 4.6 19.4 1.0 N B:ASN101 4.7 14.0 1.0 CB B:ARG67 4.8 19.6 1.0 CA B:ASN101 4.8 12.6 1.0 O B:ALA134 4.8 23.2 1.0 N B:ASP136 4.9 23.4 1.0 CG B:GLU11 4.9 19.3 1.0 CB B:GLN100 4.9 15.7 1.0 N B:ASP135 5.0 20.4 1.0 CD B:ARG67 5.0 21.7 1.0 CB B:ASP102 5.0 19.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Chicken T-Cadherin EC1 EC2


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 Chicken T-Cadherin EC1 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca220 b:24.4 occ:1.00 OE2 B:GLU68 2.5 20.7 1.0 OD1 B:ASP66 2.6 26.6 1.0 OE2 B:GLU11 2.8 24.3 1.0 OD2 B:ASP102 2.8 17.6 1.0 CD B:GLU68 3.2 22.1 1.0 CG B:ASP66 3.2 28.9 1.0 CG B:GLU68 3.2 24.2 1.0 OD2 B:ASP66 3.5 24.9 1.0 CG B:ASP102 3.5 18.2 1.0 OD1 B:ASP102 3.6 19.2 1.0 CD B:GLU11 3.7 19.3 1.0 OE1 B:GLU11 3.9 16.5 1.0 N B:ARG67 4.1 20.7 1.0 N B:GLU68 4.2 23.5 1.0 CA B:ASP66 4.3 19.5 1.0 OE1 B:GLU68 4.3 19.0 1.0 CB B:ASP66 4.3 24.4 1.0 ND2 B:ASN103 4.3 17.7 1.0 CA B:CA219 4.4 13.6 1.0 C B:ASP66 4.5 18.7 1.0 OD1 B:ASN12 4.6 15.2 1.0 CB B:GLU68 4.6 17.6 1.0 ND2 B:ASN12 4.8 19.4 1.0 CB B:ASP102 4.9 19.2 1.0 CA B:GLU68 5.0 20.2 1.0

C.Ciatto, F.Bahna, N.Zampieri, H.C.Vansteenhouse, P.S.Katsamba, G.Ahlsen, O.J.Harrison, J.Brasch, X.Jin, S.Posy, J.Vendome, B.Ranscht, T.M.Jessell, B.Honig, L.Shapiro. T-Cadherin Structures Reveal A Novel Adhesive Binding Mechanism Nat.Struct.Mol.Biol. V. 17 339 2010.
ISSN: ISSN 1545-9993
PubMed: 20190755
DOI: 10.1038/NSMB.1781