Calcium in PDB 6bxz: Crystal Structure of Pig Protocadherin-15 EC10-MAD12

The structure of Crystal Structure of Pig Protocadherin-15 EC10-MAD12, PDB code: 6bxz was solved by P.De-La-Torre, R.Araya-Secchi, D.Choudhary, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	108.18 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.284, 49.246, 108.253, 90.00, 92.15, 90.00
R / Rfree (%)	18.7 / 21.7

The binding sites of Calcium atom in the Crystal Structure of Pig Protocadherin-15 EC10-MAD12 (pdb code 6bxz). 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 Pig Protocadherin-15 EC10-MAD12, PDB code: 6bxz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1401 b:61.2 occ:1.00 OE1 C:GLU1026 2.3 62.5 1.0 OE2 C:GLU1077 2.4 66.7 1.0 OD1 C:ASP1075 2.4 65.9 1.0 OD2 C:ASP1118 2.4 68.1 1.0 O C:HOH1589 2.5 54.1 1.0 CG C:ASP1118 3.3 64.8 1.0 CG C:ASP1075 3.5 65.9 1.0 CD C:GLU1026 3.5 62.5 1.0 OD1 C:ASP1118 3.5 61.9 1.0 CD C:GLU1077 3.6 66.2 1.0 NE2 C:HIS1119 4.1 63.6 1.0 OE2 C:GLU1026 4.2 61.6 1.0 OD2 C:ASP1075 4.3 66.2 1.0 CA C:ASP1075 4.3 64.3 1.0 CB C:ASP1075 4.3 65.4 1.0 CA C:CA1402 4.3 57.0 1.0 OE1 C:GLU1077 4.4 65.2 1.0 N C:TYR1076 4.5 63.6 1.0 CG C:GLU1026 4.5 62.5 1.0 CB C:GLU1077 4.5 67.5 1.0 CG C:GLU1077 4.6 66.9 1.0 N C:GLU1077 4.6 65.7 1.0 CB C:ASP1118 4.7 64.3 1.0 C C:ASP1075 4.8 63.6 1.0 CD2 C:HIS1119 4.8 60.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1402 b:57.0 occ:1.00 OD1 C:ASP1115 2.3 61.5 1.0 O C:GLU1116 2.3 60.4 1.0 OE1 C:GLU1077 2.3 65.2 1.0 OD1 C:ASP1151 2.4 60.1 1.0 OD1 C:ASP1118 2.4 61.9 1.0 OE2 C:GLU1026 2.5 61.6 1.0 CD C:GLU1077 3.1 66.2 1.0 OE2 C:GLU1077 3.2 66.7 1.0 CD C:GLU1026 3.4 62.5 1.0 CG C:ASP1151 3.5 58.7 1.0 CG C:ASP1115 3.5 62.6 1.0 C C:GLU1116 3.5 61.1 1.0 CG C:ASP1118 3.5 64.8 1.0 OE1 C:GLU1026 3.6 62.5 1.0 N C:GLU1116 3.8 61.0 1.0 OD2 C:ASP1118 4.0 68.1 1.0 OD2 C:ASP1115 4.1 63.3 1.0 N C:ASP1118 4.2 59.5 1.0 CB C:ASP1151 4.2 58.3 1.0 CD2 C:HIS1119 4.2 60.7 1.0 CA C:GLU1116 4.2 61.7 1.0 OD2 C:ASP1151 4.3 56.1 1.0 CA C:CA1401 4.3 61.2 1.0 CA C:ASP1151 4.4 59.7 1.0 C C:ASP1115 4.5 61.7 1.0 CA C:ASP1115 4.5 62.0 1.0 CG C:GLU1077 4.6 66.9 1.0 N C:ASN1117 4.6 61.2 1.0 CB C:ASP1115 4.6 62.3 1.0 CB C:ASP1118 4.7 64.3 1.0 CB C:TYR1076 4.7 63.2 1.0 CG C:GLU1026 4.7 62.5 1.0 NE2 C:HIS1119 4.8 63.6 1.0 CA C:ASN1117 4.8 61.3 1.0 CA C:ASP1118 4.9 61.2 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1403 b:49.4 occ:1.00 O C:HIS1119 2.3 51.5 1.0 O C:TYR1155 2.3 50.0 1.0 OD2 C:ASP1205 2.4 50.6 1.0 OD1 C:ASN1117 2.4 61.5 1.0 OD2 C:ASP1151 2.5 56.1 1.0 OD1 C:ASP1149 2.6 53.0 1.0 OD2 C:ASP1149 2.8 51.7 1.0 CG C:ASP1149 3.0 53.1 1.0 CG C:ASP1205 3.3 50.1 1.0 C C:HIS1119 3.5 53.1 1.0 C C:TYR1155 3.5 51.2 1.0 CG C:ASP1151 3.5 58.7 1.0 CG C:ASN1117 3.6 62.2 1.0 CB C:ASP1151 3.9 58.3 1.0 CB C:ASP1205 4.0 48.4 1.0 OD1 C:ASP1205 4.1 50.9 1.0 N C:HIS1119 4.1 57.4 1.0 ND2 C:ASN1117 4.2 62.9 1.0 CA C:HIS1119 4.3 55.8 1.0 CB C:ASP1149 4.3 53.0 1.0 N C:SER1156 4.4 50.3 1.0 CB C:HIS1119 4.4 55.8 1.0 CA C:SER1156 4.4 48.8 1.0 CA C:TYR1155 4.5 53.4 1.0 N C:PRO1120 4.5 52.7 1.0 CA C:PRO1120 4.5 50.2 1.0 CB C:TYR1155 4.5 55.8 1.0 OD1 C:ASP1151 4.6 60.1 1.0 C C:PRO1120 4.7 48.2 1.0 CA C:ASN1117 4.7 61.3 1.0 CB C:ASN1117 4.7 61.9 1.0 CD1 C:LEU1211 4.8 58.1 1.0 N C:PRO1121 4.9 46.8 1.0 CD C:PRO1121 4.9 46.2 1.0 CB C:SER1156 4.9 49.9 1.0 C C:ASN1117 4.9 61.3 1.0 N C:ASP1118 5.0 59.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1401 b:51.0 occ:1.00 OE1 A:GLU1026 2.2 48.8 1.0 OD1 A:ASP1075 2.3 53.7 1.0 O A:HOH1627 2.3 50.6 1.0 OE2 A:GLU1077 2.4 50.0 1.0 OD2 A:ASP1118 2.4 49.9 1.0 CG A:ASP1118 3.3 47.7 1.0 CD A:GLU1026 3.3 47.8 1.0 CG A:ASP1075 3.4 55.2 1.0 OD1 A:ASP1118 3.5 45.8 1.0 CD A:GLU1077 3.6 48.9 1.0 OE2 A:GLU1026 4.0 46.6 1.0 CA A:CA1402 4.2 43.5 1.0 CA A:ASP1075 4.2 54.5 1.0 NE2 A:HIS1119 4.2 48.5 1.0 CB A:ASP1075 4.3 56.1 1.0 OD2 A:ASP1075 4.3 56.9 1.0 N A:TYR1076 4.3 51.5 1.0 OE1 A:GLU1077 4.3 47.2 1.0 CG A:GLU1026 4.4 48.4 1.0 N A:GLU1077 4.5 51.0 1.0 CB A:GLU1077 4.5 51.4 1.0 CG A:GLU1077 4.6 49.8 1.0 C A:ASP1075 4.7 53.3 1.0 CB A:ASP1118 4.7 46.9 1.0 CD2 A:HIS1119 4.8 45.7 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-MAD12


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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1402 b:43.5 occ:1.00 OE1 A:GLU1077 2.3 47.2 1.0 O A:GLU1116 2.3 41.9 1.0 OD1 A:ASP1115 2.3 47.5 1.0 OD1 A:ASP1151 2.3 43.4 1.0 OD1 A:ASP1118 2.4 45.8 1.0 OE2 A:GLU1026 2.5 46.6 1.0 CD A:GLU1077 3.0 48.9 1.0 OE2 A:GLU1077 3.1 50.0 1.0 CD A:GLU1026 3.5 47.8 1.0 CG A:ASP1151 3.5 43.5 1.0 CG A:ASP1118 3.5 47.7 1.0 C A:GLU1116 3.5 43.4 1.0 CG A:ASP1115 3.5 47.6 1.0 OE1 A:GLU1026 3.6 48.8 1.0 N A:GLU1116 3.9 45.2 1.0 OD2 A:ASP1118 4.0 49.9 1.0 CD2 A:HIS1119 4.1 45.7 1.0 N A:ASP1118 4.2 43.1 1.0 OD2 A:ASP1115 4.2 48.0 1.0 CB A:ASP1151 4.2 43.8 1.0 CA A:CA1401 4.2 51.0 1.0 CA A:GLU1116 4.3 45.2 1.0 OD2 A:ASP1151 4.3 42.1 1.0 CA A:ASP1151 4.4 44.8 1.0 CG A:GLU1077 4.5 49.8 1.0 N A:ASN1117 4.6 42.9 1.0 C A:ASP1115 4.6 46.3 1.0 CA A:ASP1115 4.6 47.6 1.0 CB A:ASP1115 4.6 47.7 1.0 NE2 A:HIS1119 4.7 48.5 1.0 CB A:ASP1118 4.7 46.9 1.0 CB A:TYR1076 4.8 48.7 1.0 CG A:GLU1026 4.8 48.4 1.0 CA A:ASN1117 4.9 42.0 1.0 CA A:ASP1118 4.9 44.3 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Pig Protocadherin-15 EC10-MAD12


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 Pig Protocadherin-15 EC10-MAD12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1403 b:37.0 occ:1.00 O A:TYR1155 2.2 38.7 1.0 O A:HIS1119 2.3 38.3 1.0 OD1 A:ASN1117 2.4 40.8 1.0 OD2 A:ASP1151 2.4 42.1 1.0 OD2 A:ASP1205 2.4 33.5 1.0 OD1 A:ASP1149 2.6 40.2 1.0 OD2 A:ASP1149 2.8 36.6 1.0 CG A:ASP1149 3.0 38.0 1.0 CG A:ASP1205 3.4 34.1 1.0 CG A:ASP1151 3.4 43.5 1.0 C A:TYR1155 3.5 40.0 1.0 C A:HIS1119 3.5 38.9 1.0 CG A:ASN1117 3.6 41.6 1.0 CB A:ASP1151 3.8 43.8 1.0 CB A:ASP1205 4.0 33.4 1.0 N A:HIS1119 4.1 41.4 1.0 OD1 A:ASP1205 4.2 34.7 1.0 ND2 A:ASN1117 4.2 41.6 1.0 CA A:HIS1119 4.2 40.8 1.0 CB A:ASP1149 4.3 37.8 1.0 N A:SER1156 4.4 39.4 1.0 CA A:TYR1155 4.4 41.5 1.0 CB A:HIS1119 4.4 41.1 1.0 CA A:SER1156 4.4 38.6 1.0 CB A:TYR1155 4.5 43.2 1.0 N A:PRO1120 4.5 38.3 1.0 OD1 A:ASP1151 4.5 43.4 1.0 CA A:PRO1120 4.6 36.3 1.0 CA A:ASN1117 4.7 42.0 1.0 CB A:ASN1117 4.7 42.1 1.0 C A:PRO1120 4.8 34.6 1.0 CD1 A:LEU1211 4.8 44.6 1.0 CB A:SER1156 4.9 39.9 1.0 C A:ASN1117 4.9 42.0 1.0 N A:ASP1118 4.9 43.1 1.0 N A:PRO1121 4.9 33.1 1.0 CD A:PRO1121 5.0 32.6 1.0

P.De-La-Torre, D.Choudhary, R.Araya-Secchi, Y.Narui, M.Sotomayor. A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15. Biophys. J. V. 115 2368 2018.
ISSN: ESSN 1542-0086
PubMed: 30527337
DOI: 10.1016/J.BPJ.2018.11.010