Calcium in PDB 6eb5: Crystal Structure of Human Protocadherin-15 EC2-3 V250N

The structure of Crystal Structure of Human Protocadherin-15 EC2-3 V250N, PDB code: 6eb5 was solved by D.Choudhary, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.47 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.184, 31.945, 115.955, 90.00, 106.40, 90.00
R / Rfree (%)	23.2 / 27

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N (pdb code 6eb5). 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 Human Protocadherin-15 EC2-3 V250N, PDB code: 6eb5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:33.7 occ:1.00 OD1 B:ASP239 2.2 45.4 1.0 OD1 B:ASP289 2.3 41.5 1.0 OE2 B:GLU202 2.3 50.4 1.0 OE1 B:GLU137 2.4 43.5 1.0 OD1 B:ASP236 2.4 47.1 1.0 O B:GLY237 2.5 46.9 1.0 OE1 B:GLU202 3.0 50.8 1.0 CD B:GLU202 3.0 51.6 1.0 CG B:ASP239 3.2 45.4 1.0 CG B:ASP289 3.3 43.1 1.0 CD B:GLU137 3.5 43.0 1.0 OD2 B:ASP239 3.6 46.9 1.0 CG B:ASP236 3.6 48.2 1.0 C B:GLY237 3.6 48.5 1.0 N B:GLY237 3.8 48.0 1.0 OE2 B:GLU137 4.0 43.7 1.0 OD2 B:ASP289 4.0 42.4 1.0 N B:ASP239 4.1 44.6 1.0 CB B:ASP289 4.2 44.5 1.0 CA B:GLY237 4.3 48.8 1.0 OD2 B:ASP236 4.3 48.2 1.0 CB B:ASP239 4.4 45.1 1.0 CA B:CA403 4.4 62.1 1.0 CG B:GLU202 4.5 53.1 1.0 CB B:TYR201 4.5 48.2 1.0 C B:ASP236 4.6 48.5 1.0 CA B:ASP236 4.7 48.4 1.0 CA B:ASP239 4.7 44.4 1.0 CG B:GLU137 4.7 42.2 1.0 N B:ASP238 4.7 49.7 1.0 CB B:ASP236 4.7 49.1 1.0 CA B:ASP289 4.8 44.9 1.0 CD1 B:LEU240 4.9 38.1 1.0 N B:LEU240 4.9 40.7 1.0 CA B:ASP238 5.0 48.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:50.8 occ:1.00 OD1 B:ASP238 2.1 49.9 1.0 O B:LEU240 2.2 38.0 1.0 OD1 B:ASP287 2.3 45.0 1.0 OD2 B:ASP289 2.3 42.4 1.0 OE1 B:GLN348 2.4 41.4 1.0 OD2 B:ASP287 2.8 48.7 1.0 CG B:ASP287 2.9 46.7 1.0 CG B:ASP238 3.3 50.9 1.0 CG B:ASP289 3.4 43.1 1.0 CD B:GLN348 3.4 42.3 1.0 C B:LEU240 3.4 38.1 1.0 NE2 B:GLN348 3.7 43.7 1.0 CB B:ASP289 3.7 44.5 1.0 CA B:ASP238 4.0 48.6 1.0 N B:LEU240 4.1 40.7 1.0 OD2 B:ASP238 4.1 54.1 1.0 CB B:ASP238 4.1 50.1 1.0 CD1 B:ILE292 4.2 54.0 1.0 CA B:LEU240 4.3 39.0 1.0 CB B:ASP287 4.4 45.3 1.0 N B:GLY241 4.4 37.5 1.0 C B:ASP238 4.4 47.0 1.0 OD1 B:ASP289 4.5 41.5 1.0 N B:ASP289 4.6 43.7 1.0 CA B:GLY241 4.6 37.5 1.0 N B:ASP239 4.6 44.6 1.0 CG B:PRO299 4.7 57.4 1.0 CG B:GLN348 4.7 42.1 1.0 CA B:ASP289 4.8 44.9 1.0 CB B:LEU240 4.8 38.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:62.1 occ:1.00 OD2 B:ASP239 2.2 46.9 1.0 OE2 B:GLU137 2.2 43.7 1.0 OD1 B:ASN200 2.3 46.1 1.0 OE1 B:GLU202 2.4 50.8 1.0 CG B:ASN200 2.8 47.1 1.0 CD B:GLU137 3.2 43.0 1.0 CG B:ASP239 3.3 45.4 1.0 ND2 B:ASN200 3.3 47.9 1.0 CD B:GLU202 3.7 51.6 1.0 OE1 B:GLU137 3.7 43.5 1.0 CB B:ASN200 3.7 46.9 1.0 CA B:ASN200 3.8 46.0 1.0 OD1 B:ASP239 3.8 45.4 1.0 N B:TYR201 3.9 46.6 1.0 C B:ASN200 4.2 45.9 1.0 N B:GLU202 4.3 52.2 1.0 CG B:GLU137 4.4 42.2 1.0 CB B:GLU202 4.4 52.8 1.0 CA B:CA401 4.4 33.7 1.0 CB B:ASP239 4.5 45.1 1.0 CG B:GLU202 4.5 53.1 1.0 OE2 B:GLU202 4.5 50.4 1.0 O B:LEU199 4.9 46.8 1.0 CB B:GLU137 4.9 41.5 1.0 CA B:TYR201 4.9 48.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Human Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:25.8 occ:1.00 OD1 A:ASP239 2.3 33.1 1.0 OD1 A:ASP289 2.3 34.6 1.0 OD1 A:ASP236 2.3 29.4 1.0 OE1 A:GLU137 2.3 31.3 1.0 O A:GLY237 2.4 31.0 1.0 OE2 A:GLU202 2.4 36.9 1.0 OE1 A:GLU202 3.1 37.2 1.0 CD A:GLU202 3.1 37.3 1.0 CG A:ASP239 3.2 34.3 1.0 CG A:ASP289 3.3 34.8 1.0 CD A:GLU137 3.5 31.5 1.0 C A:GLY237 3.6 31.7 1.0 CG A:ASP236 3.6 30.0 1.0 OD2 A:ASP239 3.6 35.7 1.0 N A:GLY237 3.7 30.4 1.0 OD2 A:ASP289 4.0 34.2 1.0 OE2 A:GLU137 4.0 31.8 1.0 N A:ASP239 4.1 33.6 1.0 CB A:ASP289 4.1 35.7 1.0 CA A:GLY237 4.2 31.1 1.0 OD2 A:ASP236 4.3 29.9 1.0 CB A:ASP239 4.4 34.5 1.0 CA A:CA403 4.5 40.9 1.0 C A:ASP236 4.5 30.8 1.0 CA A:ASP236 4.6 30.6 1.0 CB A:TYR201 4.6 31.4 1.0 CG A:GLU202 4.6 38.3 1.0 CB A:ASP236 4.6 30.2 1.0 N A:ASP238 4.7 33.3 1.0 CG A:GLU137 4.7 31.1 1.0 CA A:ASP239 4.7 34.3 1.0 O A:HOH508 4.8 17.6 1.0 CA A:ASP289 4.8 36.0 1.0 N A:LEU240 4.9 33.6 1.0 CA A:ASP238 5.0 33.2 1.0 CD1 A:LEU240 5.0 33.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Human Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.0 occ:1.00 OD1 A:ASP238 2.1 33.8 1.0 O A:LEU240 2.3 32.4 1.0 OE1 A:GLN348 2.3 31.4 1.0 O A:HOH501 2.3 39.0 1.0 OD1 A:ASP287 2.4 36.1 1.0 OD2 A:ASP289 2.4 34.2 1.0 CG A:ASP287 3.0 37.0 1.0 OD2 A:ASP287 3.0 39.2 1.0 CG A:ASP238 3.2 34.2 1.0 CD A:GLN348 3.4 31.2 1.0 CG A:ASP289 3.4 34.8 1.0 C A:LEU240 3.5 32.5 1.0 NE2 A:GLN348 3.7 30.8 1.0 CB A:ASP289 3.8 35.7 1.0 CA A:ASP238 4.0 33.2 1.0 CB A:ASP238 4.1 33.9 1.0 OD2 A:ASP238 4.1 35.3 1.0 N A:LEU240 4.2 33.6 1.0 CA A:LEU240 4.4 32.9 1.0 CB A:ASP287 4.4 36.7 1.0 N A:GLY241 4.5 32.1 1.0 C A:ASP238 4.5 33.7 1.0 OD1 A:ASP289 4.6 34.6 1.0 CA A:GLY241 4.6 31.8 1.0 N A:ASP289 4.6 35.3 1.0 CG A:PRO299 4.6 36.9 1.0 N A:ASP239 4.7 33.6 1.0 CG A:GLN348 4.7 31.8 1.0 CA A:ASP289 4.8 36.0 1.0 CB A:LEU240 4.9 33.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human Protocadherin-15 EC2-3 V250N


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 Human Protocadherin-15 EC2-3 V250N within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:40.9 occ:1.00 O A:HOH522 2.2 32.0 1.0 OD2 A:ASP239 2.2 35.7 1.0 OE1 A:GLU202 2.3 37.2 1.0 OD1 A:ASN200 2.4 32.5 1.0 OE2 A:GLU137 2.4 31.8 1.0 CG A:ASN200 3.0 33.4 1.0 CG A:ASP239 3.2 34.3 1.0 CD A:GLU137 3.4 31.5 1.0 ND2 A:ASN200 3.5 33.8 1.0 CD A:GLU202 3.5 37.3 1.0 OD1 A:ASP239 3.7 33.1 1.0 OE1 A:GLU137 3.8 31.3 1.0 CB A:ASN200 3.9 33.7 1.0 CA A:ASN200 4.0 32.9 1.0 N A:TYR201 4.2 31.6 1.0 CB A:GLU202 4.3 38.4 1.0 CG A:GLU202 4.4 38.3 1.0 N A:GLU202 4.4 36.0 1.0 C A:ASN200 4.4 32.1 1.0 CB A:ASP239 4.4 34.5 1.0 OE2 A:GLU202 4.5 36.9 1.0 CA A:CA401 4.5 25.8 1.0 CG A:GLU137 4.6 31.1 1.0

D.Choudhary, M.Sotomayor. Crystal Structure of Human Protocadherin-15 EC2-3 V250N To Be Published.