Calcium in PDB 6eet: Crystal Structure of Mouse Protocadherin-15 EC9-MAD12

The structure of Crystal Structure of Mouse Protocadherin-15 EC9-MAD12, PDB code: 6eet was solved by Y.Narui, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 3.23
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	129.507, 170.059, 91.528, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.4

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-15 EC9-MAD12 (pdb code 6eet). 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 EC9-MAD12, PDB code: 6eet:
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 EC9-MAD12


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 EC9-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1409 b:78.6 occ:1.00 OD1 A:ASP1151 2.2 0.1 1.0 OD1 A:ASP1115 2.2 83.4 1.0 O A:GLU1116 2.4 78.4 1.0 OE2 A:GLU1026 2.4 91.7 1.0 OE1 A:GLU1077 2.6 88.1 1.0 OD1 A:ASP1118 2.6 0.6 1.0 OE2 A:GLU1077 3.0 87.4 1.0 CD A:GLU1077 3.2 0.8 1.0 CG A:ASP1151 3.3 98.2 1.0 CG A:ASP1118 3.4 0.3 1.0 CG A:ASP1115 3.4 85.5 1.0 CD A:GLU1026 3.5 91.8 1.0 C A:GLU1116 3.6 82.4 1.0 N A:GLU1116 3.7 79.1 1.0 OE1 A:GLU1026 3.9 93.3 1.0 OD2 A:ASP1118 3.9 0.8 1.0 OD2 A:ASP1115 4.0 90.3 1.0 CB A:ASP1151 4.1 96.0 1.0 OD2 A:ASP1151 4.2 98.1 1.0 N A:ASP1118 4.2 94.2 1.0 CA A:GLU1116 4.2 83.6 1.0 CD2 A:HIS1119 4.3 91.0 1.0 CB A:ASP1118 4.3 94.7 1.0 CA A:CA1411 4.4 0.2 1.0 CA A:ASP1151 4.4 92.8 1.0 C A:ASP1115 4.6 82.0 1.0 CB A:ASP1115 4.6 89.8 1.0 CG A:GLU1077 4.6 0.7 1.0 N A:ASN1117 4.7 82.2 1.0 CA A:ASP1115 4.7 88.8 1.0 CG A:GLU1026 4.8 89.3 1.0 CA A:ASP1118 4.8 89.4 1.0 NE2 A:HIS1119 4.8 0.8 1.0 CB A:TYR1076 4.8 83.8 1.0 CB A:GLU1116 4.9 88.1 1.0 N A:HIS1119 5.0 90.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC9-MAD12


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 EC9-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1410 b:90.1 occ:1.00 OD2 A:ASP1149 1.8 88.8 1.0 OD1 A:ASN1117 2.3 82.6 1.0 O A:HIS1119 2.4 97.8 1.0 OD2 A:ASP1151 2.4 98.1 1.0 O A:TYR1155 2.5 82.9 1.0 OD2 A:ASP1205 2.6 69.9 1.0 CG A:ASP1149 2.7 98.7 1.0 OD1 A:ASP1149 3.0 98.2 1.0 CG A:ASN1117 3.4 82.2 1.0 CG A:ASP1151 3.4 98.2 1.0 CG A:ASP1205 3.5 68.5 1.0 C A:HIS1119 3.5 90.7 1.0 CB A:ASP1151 3.7 96.0 1.0 C A:TYR1155 3.7 78.7 1.0 ND2 A:ASN1117 4.1 86.8 1.0 OD1 A:ASP1205 4.1 58.4 1.0 CB A:ASP1149 4.1 0.9 1.0 N A:HIS1119 4.3 90.7 1.0 CA A:HIS1119 4.4 88.5 1.0 CA A:ASN1117 4.4 76.7 1.0 CB A:ASP1205 4.4 69.6 1.0 N A:PRO1120 4.5 87.9 1.0 CB A:ASN1117 4.5 74.9 1.0 CB A:TYR1155 4.5 80.9 1.0 CA A:PRO1120 4.5 80.0 1.0 OD1 A:ASP1151 4.6 0.1 1.0 CA A:TYR1155 4.6 76.8 1.0 C A:ASN1117 4.6 87.0 1.0 CB A:HIS1119 4.6 87.4 1.0 N A:SER1156 4.7 90.4 1.0 CA A:SER1156 4.8 90.3 1.0 N A:ASP1118 4.9 94.2 1.0 C A:PRO1120 4.9 75.4 1.0 CA A:ASP1151 4.9 92.8 1.0 N A:ASP1151 4.9 89.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC9-MAD12


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 EC9-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1411 b:0.2 occ:1.00 OD2 A:ASP1118 2.2 0.8 1.0 OD1 A:ASP1075 2.2 0.6 1.0 OE2 A:GLU1077 2.4 87.4 1.0 OE1 A:GLU1026 2.4 93.3 1.0 CG A:ASP1118 3.2 0.3 1.0 CD A:GLU1026 3.3 91.8 1.0 CG A:ASP1075 3.5 0.2 1.0 OE2 A:GLU1026 3.6 91.7 1.0 OD1 A:ASP1118 3.6 0.6 1.0 CD A:GLU1077 3.7 0.8 1.0 CA A:ASP1075 4.0 0.9 1.0 CB A:ASP1075 4.2 0.9 1.0 N A:TYR1076 4.2 88.5 1.0 NE2 A:HIS1119 4.3 0.8 1.0 CA A:CA1409 4.4 78.6 1.0 OD2 A:ASP1075 4.4 0.5 1.0 CG A:GLU1077 4.5 0.7 1.0 C A:ASP1075 4.5 99.9 1.0 CG A:GLU1026 4.5 89.3 1.0 CB A:ASP1118 4.5 94.7 1.0 OE1 A:GLU1077 4.5 88.1 1.0 CB A:GLU1077 4.6 0.9 1.0 N A:GLU1077 4.6 0.6 1.0 O A:LEU1074 4.7 0.6 1.0 CE1 A:HIS1119 4.7 0.2 1.0 CB A:GLU1026 4.9 87.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Mouse Protocadherin-15 EC9-MAD12


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 EC9-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1412 b:92.9 occ:1.00 O A:TYR901 2.2 79.7 1.0 OD1 A:ASN899 2.4 0.3 1.0 OD2 A:ASP933 2.4 0.7 1.0 OD1 A:ASP931 2.4 92.2 1.0 OD1 A:ASP989 2.5 0.1 1.0 O A:ALA939 2.6 97.5 1.0 OD2 A:ASP931 2.7 93.7 1.0 CG A:ASP931 2.9 91.9 1.0 OD2 A:ASP989 3.0 0.3 1.0 CG A:ASP989 3.1 0.3 1.0 CG A:ASP933 3.3 98.6 1.0 C A:TYR901 3.4 90.3 1.0 CG A:ASN899 3.5 0.8 1.0 C A:ALA939 3.7 0.1 1.0 CB A:ASP933 3.9 91.4 1.0 ND2 A:ASN899 4.0 87.7 1.0 N A:TYR901 4.0 0.4 1.0 CA A:TYR901 4.2 94.4 1.0 CA A:ALA939 4.2 0.2 1.0 OD1 A:ASP933 4.2 0.4 1.0 CB A:ASP931 4.3 85.2 1.0 CB A:ALA939 4.4 0.7 1.0 N A:PRO902 4.4 83.0 1.0 CB A:TYR901 4.5 96.5 1.0 CB A:ASP989 4.5 0.7 1.0 CA A:PRO902 4.6 85.2 1.0 CB A:ASN899 4.7 0.9 1.0 N A:ASP900 4.7 0.3 1.0 N A:SER940 4.8 0.9 1.0 CD A:PRO903 4.8 0.8 1.0 C A:PRO902 4.8 88.3 1.0 SD A:MET995 4.9 1.0 1.0

Y.Narui, M.Sotomayor. Crystal Structure of Mouse Protocadherin-15 EC9-MAD12 To Be Published.