Calcium in PDB 3ppe: Crystal Structure of Chicken Ve-Cadherin EC1-2

The structure of Crystal Structure of Chicken Ve-Cadherin EC1-2, PDB code: 3ppe was solved by J.Brasch, O.J.Harrison, G.Ahlsen, S.M.Carnally, R.M.Henderson, B.Honig, L.S.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.74 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.973, 99.973, 105.987, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.2

The binding sites of Calcium atom in the Crystal Structure of Chicken Ve-Cadherin EC1-2 (pdb code 3ppe). 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 Ve-Cadherin EC1-2, PDB code: 3ppe:
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 Ve-Cadherin EC1-2


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.7 occ:1.00 OD1 A:ASP62 2.3 11.5 1.0 OE1 A:GLU64 2.3 13.2 1.0 OD2 A:ASP99 2.3 15.8 1.0 OE1 A:GLU11 2.4 12.5 1.0 O A:HOH311 2.5 13.9 1.0 OE1 A:GLU12 2.5 17.8 1.0 CG A:ASP99 3.2 12.9 1.0 CG A:ASP62 3.3 15.6 1.0 OD1 A:ASP99 3.3 10.6 1.0 CD A:GLU11 3.3 14.2 1.0 CD A:GLU12 3.5 16.1 1.0 CD A:GLU64 3.5 13.1 1.0 OE2 A:GLU11 3.7 10.7 1.0 CG A:GLU12 3.7 12.6 1.0 OD2 A:ASP62 4.0 17.1 1.0 CA A:CA403 4.0 12.2 1.0 O A:HOH292 4.1 22.6 1.0 CA A:ASP62 4.2 15.3 1.0 O A:HOH313 4.2 19.1 1.0 CB A:ASP62 4.2 15.6 1.0 N A:ARG63 4.3 14.1 1.0 N A:GLU64 4.3 13.6 1.0 CB A:GLU64 4.4 13.9 1.0 OD1 A:ASN100 4.4 19.1 1.0 CG A:GLU64 4.4 13.0 1.0 OE2 A:GLU64 4.4 16.7 1.0 O A:HOH312 4.5 17.1 1.0 O A:HOH364 4.5 21.2 1.0 C A:ASP62 4.5 15.1 1.0 CG A:GLU11 4.6 9.8 1.0 CB A:ASP99 4.6 13.5 1.0 OE2 A:GLU12 4.6 16.7 1.0 CA A:GLU64 5.0 14.8 1.0

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


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:11.2 occ:1.00 O A:HIS139 2.3 9.6 1.0 O A:ASN100 2.3 12.9 1.0 OD2 A:ASP132 2.4 10.2 1.0 OD1 A:ASN98 2.4 14.0 1.0 OD2 A:ASP130 2.4 12.8 1.0 OD1 A:ASP130 2.6 14.1 1.0 OD1 A:ASP184 2.6 11.7 1.0 CG A:ASP130 2.8 14.3 1.0 CG A:ASP132 3.4 11.9 1.0 CG A:ASN98 3.5 11.5 1.0 C A:ASN100 3.5 13.1 1.0 C A:HIS139 3.5 10.2 1.0 CG A:ASP184 3.6 11.7 1.0 CB A:ASP184 3.8 8.6 1.0 CB A:ASP132 3.8 11.3 1.0 ND2 A:ASN98 3.9 8.1 1.0 N A:ASN100 4.2 13.8 1.0 CA A:ASN100 4.3 13.2 1.0 CB A:ASP130 4.3 13.2 1.0 CA A:HIS139 4.4 11.3 1.0 CD2 A:LEU188 4.4 18.2 1.0 N A:ALA140 4.5 11.2 1.0 N A:ALA101 4.5 13.3 1.0 OD1 A:ASP132 4.5 12.1 1.0 CA A:ALA140 4.6 11.3 1.0 CA A:ALA101 4.6 13.8 1.0 CB A:ASN100 4.6 12.2 1.0 OD2 A:ASP184 4.7 12.6 1.0 CB A:ASN98 4.7 11.4 1.0 CB A:LEU188 4.8 18.5 1.0 CA A:ASN98 4.9 11.8 1.0 CB A:HIS139 4.9 10.1 1.0 N A:ASP132 4.9 12.1 1.0 CA A:ASP132 5.0 12.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Chicken Ve-Cadherin EC1-2


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:12.2 occ:1.00 OD1 A:ASP99 2.2 10.6 1.0 OD2 A:ASP96 2.3 7.7 1.0 OE2 A:GLU11 2.3 10.7 1.0 O A:ILE97 2.4 11.4 1.0 OD1 A:ASP132 2.4 12.1 1.0 OE2 A:GLU64 2.5 16.7 1.0 OE1 A:GLU64 2.7 13.2 1.0 CD A:GLU64 3.0 13.1 1.0 CG A:ASP96 3.4 12.4 1.0 CD A:GLU11 3.4 14.2 1.0 CG A:ASP99 3.4 12.9 1.0 CG A:ASP132 3.5 11.9 1.0 C A:ILE97 3.6 11.5 1.0 OE1 A:GLU11 3.8 12.5 1.0 N A:ILE97 3.9 12.0 1.0 OD1 A:ASP96 3.9 15.9 1.0 OD1 A:ASN100 3.9 19.1 1.0 CA A:CA401 4.0 14.7 1.0 N A:ASP99 4.0 13.3 1.0 OD2 A:ASP99 4.0 15.8 1.0 CB A:ASP132 4.1 11.3 1.0 CA A:ASP132 4.2 12.5 1.0 NE A:ARG63 4.3 14.6 1.0 CA A:ILE97 4.3 11.6 1.0 CG A:GLU64 4.4 13.0 1.0 OD2 A:ASP132 4.5 10.2 1.0 CB A:ASP96 4.5 11.8 1.0 CA A:ASP96 4.6 12.7 1.0 CB A:ASP99 4.6 13.5 1.0 CG1 A:ILE97 4.6 11.1 1.0 C A:ASP96 4.6 12.6 1.0 N A:ASN98 4.6 12.0 1.0 CG A:GLU11 4.7 9.8 1.0 CA A:ASP99 4.8 13.7 1.0 CA A:ASN98 4.8 11.8 1.0 C A:ASN98 4.9 12.7 1.0 NH2 A:ARG63 4.9 12.9 1.0 CB A:ARG63 5.0 12.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Chicken Ve-Cadherin EC1-2


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:16.5 occ:1.00 OD1 B:ASP62 2.2 12.7 1.0 OE1 B:GLU64 2.4 15.7 1.0 OE1 B:GLU11 2.4 11.1 1.0 OD1 B:ASP99 2.4 12.9 1.0 O B:HOH343 2.5 16.1 1.0 OE1 B:GLU12 2.6 21.4 1.0 CG B:ASP99 3.2 14.1 1.0 OD2 B:ASP99 3.2 13.7 1.0 CG B:ASP62 3.2 15.8 1.0 CD B:GLU11 3.3 11.9 1.0 CD B:GLU12 3.5 20.2 1.0 CD B:GLU64 3.6 16.3 1.0 CG B:GLU12 3.7 16.8 1.0 OE2 B:GLU11 3.7 10.2 1.0 OD2 B:ASP62 4.0 15.7 1.0 CA B:CA403 4.0 13.7 1.0 CA B:ASP62 4.1 16.4 1.0 O B:HOH380 4.1 19.1 1.0 CB B:ASP62 4.1 16.6 1.0 N B:ARG63 4.2 15.6 1.0 O B:HOH301 4.2 19.8 1.0 CB B:GLU64 4.4 17.0 1.0 CG B:GLU64 4.4 17.0 1.0 N B:GLU64 4.4 16.0 1.0 OD1 B:ASN100 4.4 16.3 1.0 C B:ASP62 4.5 16.0 1.0 O B:HOH296 4.5 19.2 1.0 OE2 B:GLU64 4.5 16.2 1.0 CG B:GLU11 4.6 11.4 1.0 O B:HOH464 4.6 25.8 1.0 CB B:ASP99 4.6 13.8 1.0 OE2 B:GLU12 4.7 21.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Chicken Ve-Cadherin EC1-2


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:13.1 occ:1.00 O B:HIS139 2.2 14.0 1.0 O B:ASN100 2.3 14.9 1.0 OD1 B:ASN98 2.3 14.8 1.0 OD1 B:ASP184 2.4 18.4 1.0 OD2 B:ASP132 2.4 11.1 1.0 OD2 B:ASP130 2.5 13.9 1.0 OD1 B:ASP130 2.7 15.4 1.0 CG B:ASP130 2.9 16.1 1.0 CG B:ASN98 3.4 14.9 1.0 CG B:ASP184 3.4 16.1 1.0 C B:HIS139 3.5 13.6 1.0 CG B:ASP132 3.5 11.8 1.0 C B:ASN100 3.5 14.2 1.0 CB B:ASP132 3.9 12.0 1.0 CB B:ASP184 3.9 14.1 1.0 ND2 B:ASN98 3.9 9.2 1.0 N B:ASN100 4.2 13.8 1.0 CA B:HIS139 4.3 14.9 1.0 CA B:ASN100 4.3 13.7 1.0 CB B:ASP130 4.4 13.9 1.0 N B:ALA140 4.4 14.5 1.0 N B:ALA101 4.5 13.9 1.0 OD2 B:ASP184 4.5 16.9 1.0 CD2 B:LEU188 4.5 16.9 1.0 OD1 B:ASP132 4.6 11.2 1.0 CA B:ALA140 4.6 15.2 1.0 CA B:ALA101 4.6 13.6 1.0 CB B:ASN100 4.7 12.4 1.0 CB B:ASN98 4.7 13.5 1.0 CB B:HIS139 4.8 14.0 1.0 CA B:ASN98 4.8 14.1 1.0 N B:ASP132 4.9 13.0 1.0 C B:ASN98 5.0 14.6 1.0 CB B:LEU188 5.0 17.5 1.0

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


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 Ve-Cadherin EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:13.7 occ:1.00 OD2 B:ASP96 2.3 10.8 1.0 OD1 B:ASP132 2.4 11.2 1.0 OD2 B:ASP99 2.4 13.7 1.0 O B:ILE97 2.4 13.4 1.0 OE2 B:GLU11 2.4 10.2 1.0 OE2 B:GLU64 2.5 16.2 1.0 OE1 B:GLU64 2.6 15.7 1.0 CD B:GLU64 2.9 16.3 1.0 CG B:ASP96 3.4 12.2 1.0 CG B:ASP132 3.4 11.8 1.0 CD B:GLU11 3.5 11.9 1.0 CG B:ASP99 3.5 14.1 1.0 C B:ILE97 3.6 13.4 1.0 OE1 B:GLU11 3.8 11.1 1.0 N B:ILE97 3.9 12.7 1.0 OD1 B:ASN100 3.9 16.3 1.0 OD1 B:ASP96 3.9 12.7 1.0 N B:ASP99 4.0 14.1 1.0 CA B:CA401 4.0 16.5 1.0 CB B:ASP132 4.1 12.0 1.0 OD1 B:ASP99 4.1 12.9 1.0 CA B:ASP132 4.2 12.9 1.0 OD2 B:ASP132 4.4 11.1 1.0 CA B:ILE97 4.4 12.4 1.0 CG B:GLU64 4.4 17.0 1.0 NE B:ARG63 4.5 15.2 1.0 CB B:ASP96 4.5 11.8 1.0 CA B:ASP96 4.6 12.3 1.0 CG1 B:ILE97 4.6 10.5 1.0 C B:ASP96 4.6 11.9 1.0 CB B:ASP99 4.6 13.8 1.0 N B:ASN98 4.7 13.7 1.0 CG B:GLU11 4.8 11.4 1.0 CA B:ASP99 4.8 14.7 1.0 CA B:ASN98 4.8 14.1 1.0 NH2 B:ARG63 4.8 16.5 1.0 C B:ASN98 4.9 14.6 1.0

J.Brasch, O.J.Harrison, G.Ahlsen, S.M.Carnally, R.M.Henderson, B.Honig, L.Shapiro. Structure and Binding Mechanism of Vascular Endothelial Cadherin: A Divergent Classical Cadherin. J.Mol.Biol. V. 408 57 2011.
ISSN: ISSN 0022-2836
PubMed: 21269602
DOI: 10.1016/J.JMB.2011.01.031