Calcium in PDB 6cgb: Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2

The structure of Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2, PDB code: 6cgb was solved by J.Brasch, O.J.Harrison, L.Shapiro, B.Kaeser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.68 / 2.99
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.496, 81.030, 166.192, 90.00, 90.00, 90.00
R / Rfree (%)	27 / 30.1

The binding sites of Calcium atom in the Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2 (pdb code 6cgb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2, PDB code: 6cgb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:0.9 occ:1.00 OD1 A:ASP98 2.4 1.0 1.0 OE2 A:GLU66 2.4 0.2 1.0 OD1 A:ASP101 2.5 1.0 1.0 O A:ILE99 2.7 0.4 1.0 OE1 A:GLU11 2.7 0.0 1.0 OE1 A:GLU66 2.9 0.7 1.0 OD1 A:ASP134 2.9 0.1 1.0 CD A:GLU66 2.9 0.9 1.0 H A:ILE99 3.4 0.6 1.0 H A:ASP101 3.5 0.3 1.0 CD A:GLU11 3.5 0.4 1.0 HA A:ASP134 3.5 0.9 1.0 OE2 A:GLU11 3.5 0.1 1.0 OD1 A:ASN102 3.6 0.4 1.0 CG A:ASP98 3.6 0.6 1.0 HB3 A:ARG65 3.7 0.4 1.0 CG A:ASP101 3.7 0.5 1.0 C A:ILE99 3.9 0.0 1.0 HG13 A:ILE99 3.9 0.6 1.0 HA A:ASP98 4.1 0.5 1.0 CG A:ASP134 4.1 0.5 1.0 N A:ILE99 4.1 0.8 1.0 HD3 A:ARG65 4.2 0.0 1.0 OD2 A:ASP98 4.3 0.5 1.0 OD2 A:ASP101 4.3 0.1 1.0 N A:ASP101 4.3 0.1 1.0 CA A:ASP134 4.4 0.2 1.0 CG A:GLU66 4.4 0.1 1.0 HA A:ASN100 4.4 0.2 1.0 HB3 A:ASP134 4.5 0.2 1.0 CB A:ASP134 4.6 0.3 1.0 CA A:ILE99 4.6 0.4 1.0 CB A:ASP98 4.7 0.8 1.0 CB A:ARG65 4.7 0.4 1.0 HG3 A:GLU66 4.7 0.7 1.0 H A:GLU66 4.7 0.2 1.0 HG2 A:GLU66 4.7 0.7 1.0 H A:ASP135 4.7 0.7 1.0 CA A:ASP98 4.7 0.1 1.0 CG1 A:ILE99 4.7 0.3 1.0 CG A:ASN102 4.8 0.6 1.0 HG12 A:ILE99 4.8 0.6 1.0 CB A:ASP101 4.8 0.9 1.0 HB2 A:ASP98 4.9 1.0 1.0 N A:ASN100 4.9 0.6 1.0 H A:ARG65 4.9 0.2 1.0 C A:ASP98 4.9 0.3 1.0 HB2 A:ARG65 4.9 0.4 1.0 CG A:GLU11 4.9 0.2 1.0 OD1 A:ASP64 5.0 0.0 1.0 HB3 A:ASP101 5.0 0.1 1.0

Calcium binding site 2 out of 3 in the Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:0.1 occ:1.00 OD2 A:ASP101 2.3 0.1 1.0 OE2 A:GLU11 2.5 0.1 1.0 OD1 A:ASP64 2.5 0.0 1.0 CG A:ASP64 3.0 0.7 1.0 OD2 A:ASP64 3.1 0.2 1.0 OE2 A:GLU12 3.4 0.5 1.0 CG A:ASP101 3.4 0.5 1.0 OE1 A:GLU66 3.4 0.7 1.0 CD A:GLU11 3.7 0.4 1.0 HO2 A:GOL305 3.9 0.7 1.0 OD1 A:ASP101 3.9 1.0 1.0 HG2 A:GLU12 4.0 0.4 1.0 CB A:ASP64 4.1 0.9 1.0 HB2 A:ASP64 4.1 0.0 1.0 HA A:ASP64 4.2 0.1 1.0 HG2 A:GLU11 4.2 0.2 1.0 H12 A:GOL305 4.3 0.5 1.0 HD21 A:ASN102 4.3 0.3 1.0 CD A:GLU12 4.4 0.5 1.0 H32 A:GOL305 4.4 0.6 1.0 HB2 A:GLU66 4.4 0.8 1.0 CG A:GLU11 4.4 0.2 1.0 OD1 A:ASN102 4.5 0.4 1.0 HB2 A:ASP101 4.5 0.1 1.0 CG A:GLU12 4.5 0.8 1.0 HG3 A:GLU11 4.5 0.2 1.0 CD A:GLU66 4.6 0.9 1.0 HG3 A:GLU12 4.6 0.4 1.0 CB A:ASP101 4.6 0.9 1.0 H11 A:GOL305 4.7 0.5 1.0 OE1 A:GLU11 4.7 0.0 1.0 CA A:ASP64 4.7 0.6 1.0 H A:GLU66 4.7 0.2 1.0 O2 A:GOL305 4.8 0.8 1.0 C1 A:GOL305 4.9 0.4 1.0 HB3 A:ASP64 4.9 0.0 1.0 ND2 A:ASN102 5.0 0.9 1.0

Calcium binding site 3 out of 3 in the Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chimera of Mouse Cadherin-11 EC1 and Mouse Cadherin-6 EC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:0.9 occ:1.00 OD2 A:ASP134 2.3 0.9 1.0 OD2 A:ASP132 2.3 1.0 1.0 OD1 A:ASN100 2.4 0.4 1.0 OD2 A:ASP187 2.5 0.6 1.0 OD1 A:ASP132 2.5 0.3 1.0 O A:ASN102 2.7 0.8 1.0 CG A:ASP132 2.7 0.4 1.0 HB2 A:ASP134 2.9 0.2 1.0 CG A:ASP134 3.2 0.5 1.0 HA A:ALA142 3.3 0.7 1.0 CG A:ASN100 3.4 0.3 1.0 HB3 A:ASP187 3.4 0.9 1.0 CG A:ASP187 3.4 0.7 1.0 HB2 A:ASP187 3.5 0.9 1.0 CB A:ASP134 3.5 0.3 1.0 CB A:ASP187 3.7 0.4 1.0 O A:SER141 3.7 0.2 1.0 HD21 A:ASN100 3.7 0.1 1.0 HD12 A:LEU195 3.9 0.1 1.0 C A:ASN102 3.9 0.8 1.0 HD3 A:PRO104 3.9 0.5 1.0 ND2 A:ASN100 3.9 0.1 1.0 H A:ASP134 4.0 0.7 1.0 HB3 A:ASP134 4.0 0.2 1.0 H A:ASN102 4.1 0.5 1.0 CA A:ALA142 4.2 0.4 1.0 HA A:GLU103 4.2 0.5 1.0 CB A:ASP132 4.2 0.5 1.0 HB2 A:ALA142 4.3 0.4 1.0 HB2 A:ASN102 4.3 0.0 1.0 HA A:ASN100 4.3 0.2 1.0 OD1 A:ASP134 4.4 0.1 1.0 HB1 A:ALA142 4.4 0.4 1.0 CB A:ALA142 4.5 0.2 1.0 HB3 A:ASP132 4.6 0.8 1.0 OD1 A:ASP187 4.6 0.6 1.0 CB A:ASN100 4.6 0.3 1.0 HB2 A:ASP132 4.6 0.8 1.0 C A:SER141 4.6 0.8 1.0 HB2 A:LEU195 4.7 0.8 1.0 HG3 A:PRO104 4.7 0.1 1.0 N A:ASP134 4.7 0.4 1.0 CA A:ASP134 4.7 0.2 1.0 HD22 A:ASN100 4.8 0.1 1.0 CD A:PRO104 4.8 0.6 1.0 HB2 A:ASN100 4.8 0.9 1.0 N A:ASN102 4.8 0.7 1.0 CA A:GLU103 4.8 0.7 1.0 CA A:ASN102 4.8 0.1 1.0 C A:GLU103 4.8 0.3 1.0 N A:GLU103 4.8 0.5 1.0 CA A:ASN100 4.9 0.3 1.0 CD1 A:LEU195 4.9 0.7 1.0 N A:ALA142 4.9 0.8 1.0 N A:PRO104 4.9 0.9 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