Calcium in PDB 5tpk: Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A

The structure of Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A, PDB code: 5tpk was solved by C.Chen, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.17 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.796, 22.990, 70.741, 90.00, 97.27, 90.00
R / Rfree (%)	19 / 22.9

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A (pdb code 5tpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A, PDB code: 5tpk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A


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 Mouse Protocadherin-15 EC7-8 V875A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:36.8 occ:1.00 OD1 A:ASN757 2.3 33.5 1.0 OE1 A:GLU759 2.3 35.3 1.0 O A:HOH1194 2.4 39.4 1.0 OE2 A:GLU708 2.4 31.4 1.0 OD2 A:ASP793 2.4 45.6 1.0 OE2 A:GLU709 2.5 38.4 1.0 CG A:ASP793 3.3 44.4 1.0 CD A:GLU708 3.3 31.6 1.0 OD1 A:ASP793 3.4 42.1 1.0 CG A:ASN757 3.4 34.2 1.0 CD A:GLU709 3.5 36.5 1.0 CD A:GLU759 3.6 36.0 1.0 OE1 A:GLU708 3.7 32.3 1.0 CG A:GLU709 3.8 36.0 1.0 CA A:CA1002 4.0 33.2 1.0 O A:HOH1127 4.2 44.6 1.0 CA A:ASN757 4.2 31.8 1.0 ND2 A:ASN757 4.2 35.6 1.0 N A:ARG758 4.2 30.9 1.0 CB A:ASN757 4.3 33.1 1.0 O A:HOH1172 4.3 47.6 1.0 O A:HOH1185 4.3 52.4 1.0 ND2 A:ASN794 4.4 40.6 1.0 N A:GLU759 4.4 33.2 1.0 OE2 A:GLU759 4.4 35.9 1.0 CB A:GLU759 4.4 36.2 1.0 CG A:GLU759 4.4 37.0 1.0 CG A:GLU708 4.5 30.4 1.0 C A:ASN757 4.6 31.2 1.0 OE1 A:GLU709 4.6 37.0 1.0 CB A:ASP793 4.7 45.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A


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 Mouse Protocadherin-15 EC7-8 V875A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:33.2 occ:1.00 OD1 A:ASP826 2.3 39.6 1.0 OE1 A:GLU708 2.3 32.3 1.0 O A:ILE791 2.3 39.7 1.0 OD1 A:ASP793 2.4 42.1 1.0 OE2 A:GLU759 2.4 35.9 1.0 OD1 A:ASP790 2.5 40.1 1.0 OE1 A:GLU759 2.8 35.3 1.0 CD A:GLU759 3.0 36.0 1.0 CD A:GLU708 3.4 31.6 1.0 CG A:ASP790 3.4 39.8 1.0 CG A:ASP826 3.4 38.8 1.0 CG A:ASP793 3.5 44.4 1.0 C A:ILE791 3.5 40.0 1.0 OE2 A:GLU708 3.8 31.4 1.0 N A:ILE791 3.8 36.9 1.0 OD2 A:ASP790 3.8 41.7 1.0 ND2 A:ASN794 4.0 40.6 1.0 CA A:CA1001 4.0 36.8 1.0 CB A:ASP826 4.1 38.3 1.0 OD2 A:ASP793 4.1 45.6 1.0 N A:ASP793 4.1 43.1 1.0 CA A:ILE791 4.3 39.0 1.0 CA A:ASP826 4.3 38.8 1.0 OD2 A:ASP826 4.3 37.6 1.0 NE A:ARG758 4.4 35.1 1.0 CG A:GLU759 4.4 37.0 1.0 CG1 A:ILE791 4.5 40.0 1.0 N A:ASP792 4.6 48.8 1.0 CB A:ASP790 4.6 37.8 1.0 CA A:ASP790 4.6 35.9 1.0 C A:ASP790 4.7 37.0 1.0 CG A:GLU708 4.7 30.4 1.0 CB A:ASP793 4.7 45.1 1.0 NH1 A:ARG758 4.7 37.4 1.0 CA A:ASP792 4.7 45.8 1.0 CA A:ASP793 4.9 43.2 1.0 C A:ASP792 4.9 44.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A


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 Mouse Protocadherin-15 EC7-8 V875A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:34.2 occ:1.00 O A:HOH1101 2.1 33.2 1.0 O A:ASN794 2.2 36.8 1.0 OD1 A:ASP792 2.3 42.9 1.0 OD2 A:ASP826 2.4 37.6 1.0 O A:HOH1163 2.4 31.3 1.0 OD2 A:ASP824 2.5 33.7 1.0 OD1 A:ASP824 2.5 35.1 1.0 CG A:ASP824 2.9 34.0 1.0 CG A:ASP792 3.3 44.2 1.0 CG A:ASP826 3.4 38.8 1.0 C A:ASN794 3.4 37.2 1.0 CB A:ASP826 3.6 38.3 1.0 OD2 A:ASP792 3.8 45.0 1.0 N A:ASN794 4.1 39.4 1.0 OD2 A:ASP879 4.2 54.0 1.0 CA A:ASN794 4.2 38.2 1.0 CB A:ASP824 4.4 33.1 1.0 CB A:ASP792 4.4 45.9 1.0 N A:SER795 4.4 37.8 1.0 CB A:ASN794 4.5 37.5 1.0 OD1 A:ASP826 4.5 39.6 1.0 CB A:ASP879 4.6 51.6 1.0 CA A:ASP792 4.6 45.8 1.0 CA A:SER795 4.6 36.9 1.0 N A:ASP826 4.7 37.0 1.0 CB A:ALA829 4.8 41.2 1.0 CA A:ASP826 4.8 38.8 1.0 CG A:ASP879 4.9 53.5 1.0 CD A:PRO796 4.9 35.0 1.0 C A:SER795 4.9 35.3 1.0 CB A:MET884 4.9 48.5 1.0 O A:HOH1204 4.9 38.7 1.0 C A:ASP792 4.9 44.6 1.0 N A:ASP793 4.9 43.1 1.0 CG A:MET884 5.0 49.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC7-8 V875A


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 Mouse Protocadherin-15 EC7-8 V875A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:73.6 occ:1.00 O A:ASN692 2.3 71.2 1.0 OD1 A:ASN690 2.4 66.6 1.0 O A:ASN728 2.5 71.3 1.0 OD1 A:ASP722 2.6 63.4 1.0 OD2 A:ASP724 2.6 78.6 1.0 OD2 A:ASP772 2.8 62.4 1.0 OD2 A:ASP722 2.9 57.8 1.0 CG A:ASP722 3.1 59.7 1.0 CG A:ASN690 3.6 66.0 1.0 C A:ASN692 3.6 73.0 1.0 C A:ASN728 3.6 72.9 1.0 CG A:ASP724 3.6 79.9 1.0 CG A:ASP772 3.7 60.6 1.0 CB A:ASP724 4.0 78.5 1.0 CB A:ASP772 4.0 58.4 1.0 CB A:ASN728 4.1 79.6 1.0 CA A:ASN728 4.2 76.0 1.0 N A:ASN692 4.3 84.6 1.0 OD1 A:ASN692 4.3 78.7 1.0 ND2 A:ASN690 4.3 69.2 1.0 CA A:ASN692 4.5 79.0 1.0 N A:ALA693 4.5 68.3 1.0 CB A:ASP722 4.5 57.9 1.0 CA A:ASN690 4.5 61.6 1.0 CB A:ASN690 4.6 64.5 1.0 CA A:ALA693 4.6 63.6 1.0 N A:GLY729 4.6 71.6 1.0 OD1 A:ASP724 4.7 83.2 1.0 OD1 A:ASP772 4.8 61.2 1.0 CG A:ASN692 4.8 80.3 1.0 C A:ASN690 4.8 57.9 1.0 C A:ALA693 4.8 59.9 1.0 CD A:ARG778 4.9 69.9 1.0 N A:ASP691 4.9 0.5 1.0

C.Chen, M.Sotomayor. Structure of Protocadherin-15 EC7-8 To Be Published.