Calcium in PDB 6cgs: Mouse Cadherin-7 EC1-2 Adhesive Fragment

The structure of Mouse Cadherin-7 EC1-2 Adhesive Fragment, PDB code: 6cgs was solved by J.Brasch, O.J.Harrison, A.Kaczynska, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.304, 82.431, 93.546, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.9

The binding sites of Calcium atom in the Mouse Cadherin-7 EC1-2 Adhesive Fragment (pdb code 6cgs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mouse Cadherin-7 EC1-2 Adhesive Fragment, PDB code: 6cgs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:14.8 occ:1.00 OE1 A:GLU66 2.3 16.7 1.0 OE2 A:GLU11 2.3 14.0 1.0 OD2 A:ASP101 2.4 18.3 1.0 OD1 A:ASP64 2.4 17.0 1.0 OE2 A:GLU12 2.4 16.9 1.0 O A:HOH639 2.4 17.6 1.0 CG A:ASP101 3.2 17.9 1.0 CD A:GLU11 3.2 14.4 1.0 OD1 A:ASP101 3.2 15.2 1.0 CD A:GLU12 3.4 19.8 1.0 CG A:ASP64 3.4 19.2 1.0 HG3 A:GLU12 3.4 21.8 1.0 H A:GLU66 3.5 21.3 1.0 HA A:ASP64 3.5 19.2 1.0 CD A:GLU66 3.6 14.2 1.0 OE1 A:GLU11 3.6 13.3 1.0 HD21 A:ASN102 3.6 18.7 1.0 HG2 A:GLU12 3.6 21.8 1.0 HB2 A:GLU66 3.7 20.3 1.0 CG A:GLU12 3.7 18.2 1.0 H A:ARG65 3.8 17.6 1.0 CA A:CA302 4.0 14.1 1.0 O A:HOH548 4.0 29.2 1.0 OD2 A:ASP64 4.1 21.7 1.0 CA A:ASP64 4.2 16.0 1.0 N A:ARG65 4.2 14.6 1.0 CB A:ASP64 4.2 17.9 1.0 ND2 A:ASN102 4.3 15.6 1.0 N A:GLU66 4.4 17.8 1.0 HB2 A:ASP64 4.4 21.5 1.0 HD22 A:ASN102 4.4 18.7 1.0 OE2 A:GLU66 4.4 15.8 1.0 O A:HOH447 4.4 23.3 1.0 CB A:GLU66 4.5 16.9 1.0 HB2 A:GLU11 4.5 15.9 1.0 OE1 A:GLU12 4.5 18.7 1.0 CG A:GLU66 4.5 15.7 1.0 CG A:GLU11 4.5 14.5 1.0 C A:ASP64 4.5 15.1 1.0 HG3 A:GLU11 4.6 17.4 1.0 HB3 A:ARG65 4.6 19.1 1.0 CB A:ASP101 4.6 19.4 1.0 O A:HOH490 4.6 21.4 1.0 HG2 A:GLU66 4.7 18.9 1.0 HB2 A:ASP101 4.7 23.2 1.0 HG12 A:ILE99 4.8 19.0 1.0 HB3 A:ASP101 5.0 23.2 1.0

Calcium binding site 2 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:14.1 occ:1.00 OE1 A:GLU11 2.3 13.3 1.0 OD1 A:ASP98 2.3 14.2 1.0 OD1 A:ASP134 2.3 13.8 1.0 OD1 A:ASP101 2.4 15.2 1.0 OE2 A:GLU66 2.4 15.8 1.0 O A:ILE99 2.4 13.8 1.0 OE1 A:GLU66 2.7 16.7 1.0 CD A:GLU66 2.9 14.2 1.0 H A:ILE99 3.3 18.7 1.0 H A:ASP101 3.3 17.9 1.0 HD22 A:ASN102 3.3 18.7 1.0 CG A:ASP98 3.4 18.0 1.0 CD A:GLU11 3.4 14.4 1.0 CG A:ASP134 3.4 16.1 1.0 HA A:ASP134 3.5 20.3 1.0 CG A:ASP101 3.5 17.9 1.0 HE A:ARG65 3.5 19.9 1.0 C A:ILE99 3.6 16.6 1.0 OE2 A:GLU11 3.8 14.0 1.0 N A:ILE99 3.8 15.6 1.0 HD21 A:ASN102 3.9 18.7 1.0 HB3 A:ASP134 3.9 20.5 1.0 ND2 A:ASN102 3.9 15.6 1.0 HA A:ASP98 3.9 19.2 1.0 OD2 A:ASP98 3.9 18.1 1.0 CA A:CA301 4.0 14.8 1.0 HB3 A:ARG65 4.0 19.1 1.0 HG12 A:ILE99 4.0 19.0 1.0 N A:ASP101 4.1 14.9 1.0 CB A:ASP134 4.1 17.1 1.0 OD2 A:ASP101 4.1 18.3 1.0 HG13 A:ILE99 4.2 19.0 1.0 HH21 A:ARG65 4.2 20.4 1.0 HA A:ASN100 4.2 19.2 1.0 CA A:ASP134 4.2 16.9 1.0 CG A:GLU66 4.3 15.7 1.0 CA A:ILE99 4.4 15.5 1.0 OD2 A:ASP134 4.4 14.5 1.0 NE A:ARG65 4.4 16.6 1.0 HG2 A:GLU66 4.5 18.9 1.0 HG A:SER141 4.5 23.8 0.2 CG1 A:ILE99 4.5 15.8 1.0 CA A:ASP98 4.5 16.0 1.0 CB A:ASP98 4.5 17.6 1.0 H A:ASP135 4.6 23.4 1.0 N A:ASN100 4.6 16.8 1.0 HG3 A:GLU66 4.7 18.9 1.0 C A:ASP98 4.7 17.8 1.0 CB A:ASP101 4.7 19.4 1.0 CG A:GLU11 4.7 14.5 1.0 HG2 A:GLU11 4.7 17.4 1.0 H A:ASN102 4.8 19.3 1.0 CA A:ASN100 4.8 16.0 1.0 HD3 A:ARG65 4.8 19.7 1.0 CA A:ASP101 4.8 17.4 1.0 CB A:ARG65 4.9 15.9 1.0 H A:GLU66 4.9 21.3 1.0 C A:ASN100 4.9 16.3 1.0 HB3 A:ASP101 5.0 23.2 1.0 NH2 A:ARG65 5.0 17.0 1.0 HB2 A:ARG65 5.0 19.1 1.0

Calcium binding site 3 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:15.3 occ:1.00 O A:ASN102 2.3 15.3 1.0 OD1 A:ASN100 2.3 17.3 1.0 OD2 A:ASP134 2.3 14.5 1.0 O A:SER141 2.3 17.5 1.0 OD2 A:ASP187 2.4 17.2 1.0 OD2 A:ASP132 2.5 17.1 1.0 OD1 A:ASP132 2.6 17.3 1.0 CG A:ASP132 2.9 17.5 1.0 HB2 A:ASP134 3.2 20.5 1.0 CG A:ASP134 3.4 16.1 1.0 CG A:ASP187 3.4 19.4 1.0 CG A:ASN100 3.5 19.3 1.0 H A:ASN102 3.5 19.3 1.0 C A:ASN102 3.5 15.8 1.0 C A:SER141 3.6 21.9 1.0 HD12 A:LEU195 3.7 23.2 1.0 HB3 A:ASP187 3.7 22.1 1.0 HA A:ALA142 3.8 23.4 1.0 CB A:ASP134 3.8 17.1 1.0 HD21 A:ASN100 3.8 24.4 1.0 OG A:SER141 3.8 19.9 0.2 HB2 A:ASN102 3.9 19.5 1.0 HB2 A:ASP187 3.9 22.1 1.0 HD3 A:PRO104 3.9 19.3 1.0 CB A:ASP187 3.9 18.4 1.0 HB3 A:SER141 4.0 25.6 0.8 HA A:GLU103 4.0 19.2 0.7 ND2 A:ASN100 4.1 20.3 1.0 H A:ASP134 4.1 18.0 1.0 HA A:ASN100 4.1 19.2 1.0 N A:ASN102 4.1 16.1 1.0 HB2 A:LEU195 4.1 24.5 1.0 CA A:ASN102 4.2 16.4 1.0 HA A:SER141 4.3 26.1 1.0 HB3 A:ASP134 4.3 20.5 1.0 HG A:SER141 4.4 23.8 0.2 CB A:ASP132 4.4 17.3 1.0 OD1 A:ASP187 4.4 21.8 1.0 CA A:SER141 4.4 21.8 0.8 CA A:SER141 4.4 21.8 0.2 CB A:ASN102 4.5 16.3 1.0 OD1 A:ASP134 4.5 13.8 1.0 N A:ALA142 4.5 19.6 1.0 N A:GLU103 4.5 17.8 1.0 CA A:ALA142 4.6 19.5 1.0 CB A:ASN100 4.6 17.3 1.0 CA A:GLU103 4.6 16.0 1.0 HB2 A:ALA142 4.7 25.4 1.0 CD1 A:LEU195 4.7 19.3 1.0 CB A:SER141 4.7 21.3 0.8 CB A:SER141 4.7 21.3 0.2 CA A:ASN100 4.7 16.0 1.0 HB3 A:ASN102 4.7 19.5 1.0 HB2 A:ASP132 4.8 20.8 1.0 HB3 A:ASP132 4.8 20.8 1.0 CD A:PRO104 4.8 16.1 1.0 N A:ASP134 4.8 15.0 1.0 HG3 A:PRO104 4.8 20.0 1.0 H A:ASP101 4.9 17.9 1.0 C A:GLU103 4.9 16.0 1.0 HD22 A:ASN100 4.9 24.4 1.0 HB2 A:ASN100 4.9 20.7 1.0 C A:ASN100 4.9 16.3 1.0 CA A:ASP134 5.0 16.9 1.0

Calcium binding site 4 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:18.3 occ:1.00 OD1 B:ASP98 2.3 20.1 1.0 OE1 B:GLU11 2.3 19.3 1.0 OD1 B:ASP134 2.3 19.5 1.0 OD1 B:ASP101 2.4 18.7 1.0 O B:ILE99 2.4 20.0 1.0 OE2 B:GLU66 2.5 20.8 1.0 OE1 B:GLU66 2.8 19.1 1.0 CD B:GLU66 2.9 21.8 1.0 H B:ILE99 3.2 23.7 1.0 HD22 B:ASN102 3.2 25.3 1.0 H B:ASP101 3.3 21.8 1.0 CG B:ASP134 3.4 22.9 1.0 CD B:GLU11 3.4 19.8 1.0 HA B:ASP134 3.4 27.6 1.0 CG B:ASP98 3.4 22.2 1.0 CG B:ASP101 3.5 20.6 1.0 HE B:ARG65 3.5 25.7 0.6 C B:ILE99 3.6 18.3 1.0 HB3 B:ASP134 3.7 25.0 1.0 N B:ILE99 3.8 19.8 1.0 OE2 B:GLU11 3.8 17.6 1.0 ND2 B:ASN102 3.9 21.1 1.0 HB3 B:ARG65 3.9 22.6 0.4 HB3 B:ARG65 3.9 22.5 0.6 HA B:ASP98 3.9 22.9 1.0 HD21 B:ASN102 3.9 25.3 1.0 HD3 B:ARG65 3.9 24.9 0.4 CB B:ASP134 4.0 20.8 1.0 CA B:CA302 4.0 19.8 1.0 OD2 B:ASP98 4.0 21.5 1.0 HG13 B:ILE99 4.1 27.9 1.0 HG12 B:ILE99 4.1 27.9 1.0 HH11 B:ARG65 4.1 28.1 0.4 OD2 B:ASP101 4.1 21.6 1.0 N B:ASP101 4.1 18.1 1.0 CA B:ASP134 4.1 23.0 1.0 HA B:ASN100 4.3 24.0 1.0 HD3 B:ARG65 4.3 24.9 0.6 CA B:ILE99 4.3 21.5 1.0 OD2 B:ASP134 4.3 19.3 1.0 CG B:GLU66 4.4 22.0 1.0 NE B:ARG65 4.4 21.4 0.6 CG1 B:ILE99 4.5 23.3 1.0 CA B:ASP98 4.5 19.1 1.0 CB B:ASP98 4.5 19.6 1.0 HG2 B:GLU66 4.5 26.4 1.0 C B:ASP98 4.6 20.5 1.0 N B:ASN100 4.6 21.9 1.0 CB B:ASP101 4.7 22.5 1.0 CG B:GLU11 4.7 18.6 1.0 H B:ASP135 4.7 29.0 1.0 HG3 B:GLU66 4.7 26.4 1.0 HG2 B:GLU11 4.7 22.3 1.0 NH1 B:ARG65 4.8 23.4 0.4 CB B:ARG65 4.8 18.8 0.6 CA B:ASN100 4.8 20.0 1.0 H B:ASN102 4.8 24.9 1.0 CB B:ARG65 4.8 18.8 0.4 CA B:ASP101 4.8 20.3 1.0 CD B:ARG65 4.8 20.7 0.6 HB2 B:ASP134 4.9 25.0 1.0 CD B:ARG65 4.9 20.7 0.4 HB2 B:ARG65 4.9 22.5 0.6 HB2 B:ASP98 4.9 23.5 1.0 HB3 B:ASP101 4.9 27.1 1.0 C B:ASN100 5.0 21.1 1.0 HB2 B:ASN102 5.0 25.9 1.0 HG3 B:GLU11 5.0 22.3 1.0 N B:ASP134 5.0 21.5 1.0

Calcium binding site 5 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.8 occ:1.00 OD1 B:ASP64 2.2 21.9 1.0 O B:HOH576 2.3 21.3 1.0 OE1 B:GLU66 2.3 19.1 1.0 OE2 B:GLU11 2.4 17.6 1.0 OD2 B:ASP101 2.4 21.6 1.0 OE2 B:GLU12 2.4 23.0 1.0 CG B:ASP101 3.2 20.6 1.0 CG B:ASP64 3.3 25.0 1.0 OD1 B:ASP101 3.3 18.7 1.0 CD B:GLU11 3.3 19.8 1.0 CD B:GLU12 3.4 21.9 1.0 H B:GLU66 3.4 23.2 1.0 HG3 B:GLU12 3.4 25.0 1.0 HG2 B:GLU12 3.5 25.0 1.0 HB2 B:GLU66 3.5 25.1 1.0 HD21 B:ASN102 3.5 25.3 1.0 CD B:GLU66 3.6 21.8 1.0 HA B:ASP64 3.6 24.7 1.0 CG B:GLU12 3.7 20.8 1.0 OE1 B:GLU11 3.7 19.3 1.0 H B:ARG65 3.7 23.5 1.0 CA B:CA301 4.0 18.3 1.0 OD2 B:ASP64 4.0 26.2 1.0 N B:ARG65 4.2 19.6 1.0 O B:HOH536 4.2 31.4 1.0 ND2 B:ASN102 4.2 21.1 1.0 O B:HOH470 4.2 28.1 1.0 CA B:ASP64 4.3 20.6 1.0 CB B:ASP64 4.3 21.8 1.0 N B:GLU66 4.3 19.3 1.0 CB B:GLU66 4.3 21.0 1.0 HD22 B:ASN102 4.3 25.3 1.0 HB2 B:GLU11 4.4 22.9 1.0 OE2 B:GLU66 4.4 20.8 1.0 HB3 B:ARG65 4.4 22.6 0.4 HB3 B:ARG65 4.5 22.5 0.6 CG B:GLU66 4.5 22.0 1.0 HB2 B:ASP64 4.5 26.1 1.0 C B:ASP64 4.5 18.1 1.0 CG B:GLU11 4.6 18.6 1.0 O B:HOH428 4.6 28.3 1.0 OE1 B:GLU12 4.6 22.9 1.0 CB B:ASP101 4.7 22.5 1.0 HG3 B:GLU11 4.7 22.3 1.0 HG2 B:GLU66 4.7 26.4 1.0 HB2 B:ASP101 4.8 27.1 1.0 HG12 B:ILE99 4.9 27.9 1.0 CA B:GLU66 5.0 20.6 1.0

Calcium binding site 6 out of 6 in the Mouse Cadherin-7 EC1-2 Adhesive Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mouse Cadherin-7 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:20.9 occ:1.00 OD1 B:ASN100 2.3 20.7 1.0 O B:ASN102 2.4 21.9 1.0 O B:SER141 2.4 22.8 1.0 OD2 B:ASP187 2.4 20.9 1.0 OD2 B:ASP134 2.4 19.3 1.0 OD2 B:ASP132 2.4 24.4 1.0 OD1 B:ASP132 2.6 23.1 1.0 CG B:ASP132 2.8 24.6 1.0 HB2 B:ASP134 3.3 25.0 1.0 CG B:ASP187 3.4 24.9 1.0 CG B:ASN100 3.5 21.1 1.0 CG B:ASP134 3.5 22.9 1.0 H B:ASN102 3.5 24.9 1.0 C B:ASN102 3.6 23.8 1.0 C B:SER141 3.6 24.4 1.0 HB3 B:ASP187 3.7 27.9 1.0 HD12 B:LEU195 3.7 30.0 1.0 HA B:ALA142 3.8 27.8 1.0 HB2 B:ASP187 3.8 27.9 1.0 HD21 B:ASN100 3.8 27.9 1.0 HD3 B:PRO104 3.9 27.3 1.0 CB B:ASP187 3.9 23.2 1.0 CB B:ASP134 3.9 20.8 1.0 HB3 B:SER141 4.0 27.0 1.0 HB2 B:ASN102 4.0 25.9 1.0 ND2 B:ASN100 4.1 23.2 1.0 HA B:ASN100 4.1 24.0 1.0 HB2 B:LEU195 4.2 28.5 1.0 H B:ASP134 4.2 25.8 1.0 N B:ASN102 4.2 20.8 1.0 HA B:SER141 4.2 29.2 1.0 HA B:GLU103 4.3 28.4 1.0 CA B:ASN102 4.3 20.7 1.0 CB B:ASP132 4.4 24.8 1.0 CA B:SER141 4.4 24.3 1.0 OD1 B:ASP187 4.4 24.0 1.0 HB3 B:ASP134 4.5 25.0 1.0 N B:ALA142 4.5 23.4 1.0 CA B:ALA142 4.6 23.2 1.0 OD1 B:ASP134 4.6 19.5 1.0 N B:GLU103 4.6 23.9 1.0 CB B:ASN102 4.6 21.6 1.0 CB B:ASN100 4.6 21.4 1.0 CD1 B:LEU195 4.6 25.0 1.0 CB B:SER141 4.7 22.5 1.0 HB2 B:ALA142 4.7 34.1 1.0 HB2 B:ASP132 4.7 29.8 1.0 CA B:ASN100 4.7 20.0 1.0 HB3 B:ASP132 4.7 29.8 1.0 CD B:PRO104 4.8 22.7 1.0 CA B:GLU103 4.8 23.6 1.0 HG3 B:PRO104 4.8 25.2 1.0 HB3 B:ASN102 4.9 25.9 1.0 H B:ASP101 4.9 21.8 1.0 HB2 B:ASN100 4.9 25.7 1.0 N B:ASP134 4.9 21.5 1.0 HD22 B:ASN100 4.9 27.9 1.0 C B:ASN100 4.9 21.1 1.0 C B:GLU103 4.9 24.2 1.0

J.Brasch, P.S.Katsamba, O.J.Harrison, G.Ahlsen, R.B.Troyanovsky, I.Indra, A.Kaczynska, B.Kaeser, S.Troyanovsky, B.Honig, L.Shapiro. Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior. Cell Rep V. 23 1840 2018.
ISSN: ESSN 2211-1247
PubMed: 29742438
DOI: 10.1016/J.CELREP.2018.04.012