Calcium in PDB 4oy9: Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation

The structure of Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation, PDB code: 4oy9 was solved by A.Dalle Vedove, A.P.Lucarelli, V.Nardone, A.Matino, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.381, 40.949, 72.409, 90.00, 98.05, 90.00
R / Rfree (%)	16.3 / 20.2

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation (pdb code 4oy9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation, PDB code: 4oy9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation


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 Human P-Cadherin EC1-EC2 in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.1 occ:1.00 O A:HIS104 2.2 20.8 1.0 OD1 A:ASN102 2.3 22.4 1.0 O A:ASN143 2.3 18.9 1.0 OD2 A:ASP136 2.3 18.4 1.0 OD1 A:ASP195 2.4 20.9 1.0 OD2 A:ASP134 2.4 18.9 1.0 OD1 A:ASP134 2.6 20.0 1.0 CG A:ASP134 2.9 18.1 1.0 CG A:ASP195 3.3 20.0 1.0 CG A:ASP136 3.4 18.8 1.0 CG A:ASN102 3.4 21.2 1.0 C A:HIS104 3.4 22.4 1.0 C A:ASN143 3.5 16.9 1.0 CB A:ASP195 3.7 18.5 1.0 CB A:ASP136 3.7 17.0 1.0 ND2 A:ASN102 4.0 22.6 1.0 N A:HIS104 4.1 21.6 1.0 CA A:HIS104 4.1 21.2 1.0 O A:HOH650 4.2 30.8 1.0 CB A:ASP134 4.3 17.4 1.0 CB A:HIS104 4.4 21.2 1.0 N A:GLY144 4.4 17.0 1.0 OD2 A:ASP195 4.4 19.3 1.0 CA A:ASN143 4.5 18.0 1.0 N A:LYS105 4.5 22.5 1.0 CA A:GLY144 4.5 18.3 1.0 OD1 A:ASP136 4.5 18.2 1.0 CB A:ASN102 4.6 19.7 1.0 CA A:LYS105 4.7 21.9 1.0 CB A:ASN143 4.7 19.9 1.0 CA A:ASN102 4.7 18.6 1.0 N A:ASP136 4.8 18.0 1.0 C A:LYS105 4.8 22.1 1.0 N A:ASP103 4.8 17.9 1.0 CA A:ASP136 4.9 17.5 1.0 C A:ASN102 4.9 22.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation


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 Human P-Cadherin EC1-EC2 in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:20.3 occ:1.00 OD1 A:ASP136 2.2 18.2 1.0 OD1 A:ASP100 2.3 22.3 1.0 O A:GLN101 2.3 21.3 1.0 OD1 A:ASP103 2.3 22.2 1.0 OE2 A:GLU11 2.4 22.1 1.0 OE2 A:GLU69 2.4 22.8 1.0 OE1 A:GLU69 3.0 24.6 1.0 CD A:GLU69 3.1 21.5 1.0 CG A:ASP100 3.3 23.5 1.0 CG A:ASP136 3.4 18.8 1.0 CG A:ASP103 3.4 23.3 1.0 CD A:GLU11 3.5 21.0 1.0 C A:GLN101 3.5 20.4 1.0 OD2 A:ASP100 3.8 24.4 1.0 OE1 A:GLU11 3.9 22.3 1.0 N A:GLN101 3.9 21.6 1.0 N A:ASP103 4.0 17.9 1.0 OD2 A:ASP103 4.0 24.9 1.0 CA A:CA403 4.1 24.6 1.0 CD2 A:HIS104 4.1 28.1 1.0 CB A:ASP136 4.1 17.0 1.0 CA A:GLN101 4.3 23.2 1.0 OD2 A:ASP136 4.3 18.4 1.0 CA A:ASP136 4.4 17.5 1.0 NE A:ARG68 4.4 29.6 1.0 CG A:GLU69 4.5 22.8 1.0 N A:ASN102 4.5 18.9 1.0 CB A:ASP103 4.5 20.4 1.0 CB A:ASP100 4.6 21.3 1.0 NH2 A:ARG68 4.7 26.7 1.0 CA A:ASP100 4.7 20.9 1.0 CA A:ASN102 4.7 18.6 1.0 CA A:ASP103 4.7 19.9 1.0 CG A:GLU11 4.7 22.1 1.0 C A:ASP100 4.8 24.2 1.0 C A:ASN102 4.8 22.6 1.0 NE2 A:HIS104 4.8 32.4 1.0 N A:HIS104 5.0 21.6 1.0 CB A:GLN101 5.0 24.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human P-Cadherin EC1-EC2 in Closed Conformation


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 Human P-Cadherin EC1-EC2 in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:24.6 occ:1.00 O A:HOH698 2.3 27.7 1.0 OD2 A:ASP103 2.3 24.9 1.0 OE1 A:GLU69 2.3 24.6 1.0 OD1 A:ASP67 2.3 24.4 1.0 OE1 A:GLU11 2.4 22.3 1.0 O A:HOH697 2.4 24.1 1.0 CG A:ASP103 3.1 23.3 1.0 OD1 A:ASP103 3.2 22.2 1.0 CG A:ASP67 3.3 28.0 1.0 CD A:GLU11 3.3 21.0 1.0 CD A:GLU69 3.6 21.5 1.0 OE2 A:GLU11 3.7 22.1 1.0 OD2 A:ASP67 4.1 31.7 1.0 N A:ARG68 4.1 23.6 1.0 NE2 A:HIS104 4.1 32.4 1.0 CA A:CA402 4.1 20.3 1.0 CA A:ASP67 4.1 22.9 1.0 CB A:ASP67 4.2 25.4 1.0 O A:HOH680 4.3 43.8 1.0 N A:GLU69 4.3 25.5 1.0 OE2 A:GLU69 4.3 22.8 1.0 OD1 A:ASN12 4.3 26.0 1.0 C A:ASP67 4.4 21.7 1.0 O A:HOH667 4.4 36.3 1.0 CB A:GLU69 4.5 24.1 1.0 ND2 A:ASN12 4.5 24.0 1.0 CD2 A:HIS104 4.5 28.1 1.0 CG A:GLU69 4.6 22.8 1.0 CB A:ASP103 4.6 20.4 1.0 CG A:GLU11 4.6 22.1 1.0 CG A:ASN12 4.8 24.2 1.0 CB A:GLU11 5.0 21.9 1.0 CA A:ARG68 5.0 24.1 1.0

A.Dalle Vedove, A.P.Lucarelli, V.Nardone, A.Matino, E.Parisini. The X-Ray Structure of Human P-Cadherin EC1-EC2 in A Closed Conformation Provides Insight Into the Type I Cadherin Dimerization Pathway Acta Crystallogr.,Sect.F V. 71 2015.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X15003878