Calcium in PDB 6cg6: Mouse Cadherin-10 EC1-2 Adhesive Fragment

The structure of Mouse Cadherin-10 EC1-2 Adhesive Fragment, PDB code: 6cg6 was solved by J.Brasch, O.J.Harrison, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 2.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.524, 87.524, 67.758, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 28.3

The binding sites of Calcium atom in the Mouse Cadherin-10 EC1-2 Adhesive Fragment (pdb code 6cg6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Mouse Cadherin-10 EC1-2 Adhesive Fragment, PDB code: 6cg6:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Mouse Cadherin-10 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-10 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:47.8 occ:1.00 OD1 A:ASP101 2.3 52.4 1.0 O A:ILE99 2.4 52.4 1.0 OE2 A:GLU66 2.4 54.2 1.0 OD1 A:ASP134 2.4 52.7 1.0 OD1 A:ASP98 2.5 52.4 1.0 OE1 A:GLU11 2.5 54.1 1.0 OE1 A:GLU66 2.7 60.2 1.0 CD A:GLU66 2.8 58.9 1.0 H A:ILE99 3.2 63.1 1.0 H A:ASP101 3.2 62.9 1.0 CG A:ASP98 3.4 53.1 1.0 CG A:ASP101 3.4 53.1 1.0 HA A:ASP134 3.4 71.4 1.0 HE A:ARG65 3.5 82.8 1.0 CG A:ASP134 3.5 56.1 1.0 C A:ILE99 3.6 48.6 1.0 CD A:GLU11 3.6 61.5 1.0 OD1 A:ASN102 3.8 57.7 1.0 OD2 A:ASP98 3.8 55.4 1.0 N A:ILE99 3.8 52.6 1.0 HG13 A:ILE99 3.9 61.4 1.0 N A:ASP101 4.0 52.4 1.0 OD2 A:ASP101 4.0 53.4 1.0 HB3 A:ASP134 4.1 69.9 1.0 HH21 A:ARG65 4.1 71.9 1.0 HA A:ASP98 4.1 63.9 1.0 HB3 A:ARG65 4.1 74.8 1.0 CA A:CA302 4.2 56.7 1.0 HG12 A:ILE99 4.2 61.4 1.0 CB A:ASP134 4.2 58.2 1.0 OE2 A:GLU11 4.2 60.4 1.0 HA A:ASN100 4.2 66.5 1.0 CA A:ASP134 4.2 59.5 1.0 CG A:GLU66 4.3 62.0 1.0 NE A:ARG65 4.3 69.0 1.0 CA A:ILE99 4.3 51.6 1.0 HG2 A:GLU66 4.4 74.5 1.0 OD2 A:ASP134 4.5 60.7 1.0 CG1 A:ILE99 4.5 51.1 1.0 CB A:ASP98 4.5 59.1 1.0 CB A:ASP101 4.5 50.3 1.0 N A:ASN100 4.6 51.7 1.0 HG3 A:GLU66 4.6 74.5 1.0 CA A:ASP98 4.6 53.3 1.0 H A:ASP135 4.6 75.0 1.0 CA A:ASP101 4.7 52.1 1.0 H A:GLU66 4.7 76.6 1.0 C A:ASP98 4.7 48.1 1.0 HG2 A:GLU11 4.7 77.6 1.0 HB2 A:ASN102 4.7 66.1 1.0 HB3 A:ASP101 4.7 60.3 1.0 CA A:ASN100 4.8 55.4 1.0 CG A:GLU11 4.8 64.7 1.0 HB2 A:ASP98 4.8 70.9 1.0 NH2 A:ARG65 4.8 59.9 1.0 CG A:ASN102 4.9 53.0 1.0 HD3 A:ARG65 4.9 70.2 1.0 C A:ASN100 4.9 52.4 1.0 C A:ASP101 4.9 52.0 1.0

Calcium binding site 2 out of 3 in the Mouse Cadherin-10 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-10 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:56.7 occ:1.00 OD1 A:ASP64 2.2 58.5 1.0 OD2 A:ASP101 2.3 53.4 1.0 OE1 A:GLU66 2.4 60.2 1.0 OE2 A:GLU12 2.6 65.6 1.0 OE2 A:GLU11 2.8 60.4 1.0 CG A:ASP101 3.1 53.1 1.0 CG A:ASP64 3.2 62.9 1.0 OD1 A:ASP101 3.3 52.4 1.0 H A:GLU66 3.4 76.6 1.0 HB2 A:GLU66 3.4 76.5 1.0 CD A:GLU11 3.5 61.5 1.0 HG3 A:GLU12 3.6 78.4 1.0 CD A:GLU12 3.6 67.9 1.0 CD A:GLU66 3.6 58.9 1.0 HA A:ASP64 3.7 73.3 1.0 HG2 A:GLU12 3.7 78.4 1.0 OE1 A:GLU11 3.7 54.1 1.0 H A:ARG65 3.8 75.0 1.0 CG A:GLU12 3.9 65.3 1.0 OD2 A:ASP64 3.9 63.2 1.0 OD1 A:ASN102 3.9 57.7 1.0 CA A:CA301 4.2 47.8 1.0 CB A:ASP64 4.2 64.9 1.0 CB A:GLU66 4.2 63.7 1.0 N A:GLU66 4.3 63.9 1.0 N A:ARG65 4.3 62.5 1.0 CA A:ASP64 4.3 61.1 1.0 HB2 A:ASP64 4.3 77.8 1.0 CG A:GLU66 4.4 62.0 1.0 HG2 A:GLU66 4.4 74.5 1.0 CB A:ASP101 4.5 50.3 1.0 OE2 A:GLU66 4.5 54.2 1.0 C A:ASP64 4.6 60.2 1.0 HO5 A:TAM305 4.6 94.2 1.0 HB2 A:ASP101 4.6 60.3 1.0 HN2 A:TAM305 4.6 84.0 1.0 OE1 A:GLU12 4.7 85.2 1.0 HB3 A:ARG65 4.7 74.8 1.0 O A:ASP101 4.8 56.3 1.0 CG A:GLU11 4.8 64.7 1.0 HG3 A:GLU11 4.9 77.6 1.0 CA A:GLU66 4.9 65.9 1.0 HD21 A:ASN102 4.9 73.5 1.0 HB3 A:GLU66 5.0 76.5 1.0 HB3 A:ASP101 5.0 60.3 1.0

Calcium binding site 3 out of 3 in the Mouse Cadherin-10 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-10 EC1-2 Adhesive Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:53.5 occ:1.00 O A:ASN102 2.3 54.8 1.0 OD2 A:ASP132 2.3 52.3 1.0 OD2 A:ASP187 2.4 47.0 1.0 OD2 A:ASP134 2.4 60.7 1.0 OD1 A:ASN100 2.4 56.1 1.0 O A:SER141 2.4 59.9 1.0 OD1 A:ASP132 2.6 54.1 1.0 CG A:ASP132 2.8 55.3 1.0 CG A:ASP187 3.3 45.6 1.0 C A:ASN102 3.4 58.3 1.0 H A:ASN102 3.5 65.4 1.0 CG A:ASP134 3.5 56.1 1.0 HB3 A:ASP187 3.5 59.5 1.0 CG A:ASN100 3.6 50.1 1.0 HB2 A:ASP134 3.6 69.9 1.0 HB2 A:ASP187 3.6 59.5 1.0 C A:SER141 3.6 67.3 1.0 HD12 A:LEU195 3.7 67.1 1.0 CB A:ASP187 3.7 49.6 1.0 HD3 A:PRO104 3.7 61.6 1.0 HA A:ALA142 3.9 64.7 1.0 HA A:GLU103 3.9 79.1 1.0 HD21 A:ASN100 3.9 60.8 1.0 HB2 A:ASN102 4.0 66.1 1.0 CB A:ASP134 4.1 58.2 1.0 HB3 A:SER141 4.1 72.9 1.0 HB2 A:LEU195 4.1 70.1 1.0 N A:ASN102 4.2 54.5 1.0 HA A:SER141 4.2 72.8 1.0 ND2 A:ASN100 4.2 50.7 1.0 CA A:ASN102 4.3 60.6 1.0 HA A:ASN100 4.3 66.5 1.0 CB A:ASP132 4.3 59.3 1.0 H A:ASP134 4.3 64.5 1.0 OD1 A:ASP187 4.4 49.0 1.0 N A:GLU103 4.4 56.0 1.0 CA A:SER141 4.4 60.6 1.0 HG3 A:PRO104 4.5 57.9 1.0 OD1 A:ASP134 4.5 52.7 1.0 CA A:GLU103 4.5 65.9 1.0 CB A:ASN102 4.5 55.1 1.0 CD A:PRO104 4.6 51.4 1.0 CD1 A:LEU195 4.6 56.0 1.0 N A:ALA142 4.6 66.2 1.0 HB2 A:ASP132 4.6 71.1 1.0 HB3 A:ASP134 4.7 69.9 1.0 HB3 A:ASP132 4.7 71.1 1.0 HG A:LEU195 4.7 63.9 1.0 HB3 A:ASN102 4.7 66.1 1.0 CA A:ALA142 4.7 53.9 1.0 C A:GLU103 4.7 73.9 1.0 N A:PRO104 4.8 56.4 1.0 CB A:ASN100 4.8 55.8 1.0 CB A:SER141 4.8 60.7 1.0 CA A:ASN100 4.9 55.4 1.0 H A:ASP101 4.9 62.9 1.0 HA A:ASP132 4.9 61.4 1.0 CB A:LEU195 5.0 58.4 1.0 HD11 A:LEU195 5.0 67.1 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