Calcium in PDB 5uly: Crystal Structure of Human Protocadherin-15 EC2-3

The structure of Crystal Structure of Human Protocadherin-15 EC2-3, PDB code: 5uly was solved by L.N.Wimalasena, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.761, 147.625, 77.034, 90.00, 101.16, 90.00
R / Rfree (%)	21.5 / 24.6

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC2-3 (pdb code 5uly). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-15 EC2-3, PDB code: 5uly:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:35.1 occ:1.00 OD1 A:ASP236 2.2 39.7 1.0 O A:HOH1127 2.3 36.1 1.0 OE2 A:GLU137 2.3 44.7 1.0 OD1 A:ASP239 2.4 40.7 1.0 OD1 A:ASP289 2.4 37.9 1.0 O A:GLY237 2.4 34.6 1.0 CD A:GLU137 3.2 43.8 1.0 CG A:ASP289 3.3 37.1 1.0 CG A:ASP236 3.5 39.1 1.0 OE1 A:GLU137 3.5 46.3 1.0 C A:GLY237 3.6 36.9 1.0 CG A:ASP239 3.6 39.2 1.0 N A:GLY237 3.8 39.6 1.0 OD2 A:ASP289 3.9 36.6 1.0 OD2 A:ASP236 4.1 39.5 1.0 CB A:ASP289 4.1 38.8 1.0 N A:ASP239 4.3 34.6 1.0 CA A:GLY237 4.3 38.6 1.0 OD2 A:ASP239 4.4 42.0 1.0 CB A:TYR201 4.5 41.6 1.0 CG A:GLU137 4.5 44.9 1.0 CD1 A:LEU240 4.6 36.7 1.0 C A:ASP236 4.6 36.0 1.0 CG A:LEU240 4.6 36.4 1.0 O A:HOH1107 4.6 31.3 1.0 CA A:ASP236 4.6 37.0 1.0 CB A:ASP236 4.6 38.4 1.0 CA A:ASP289 4.7 40.0 1.0 CB A:ASP239 4.7 38.1 1.0 N A:ASP238 4.7 37.0 1.0 N A:LEU240 4.9 35.1 1.0 CA A:ASP239 4.9 36.1 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:46.1 occ:1.00 OD1 A:ASP238 2.2 32.5 1.0 O A:LEU240 2.3 35.6 1.0 O A:HOH1104 2.3 30.5 1.0 OE1 A:GLN348 2.4 36.5 1.0 OD1 A:ASP287 2.5 48.1 1.0 OD2 A:ASP289 2.5 36.6 1.0 OD2 A:ASP287 2.8 46.0 1.0 CG A:ASP287 3.0 45.4 1.0 CG A:ASP238 3.3 34.4 1.0 CD A:GLN348 3.4 37.4 1.0 CG A:ASP289 3.4 37.1 1.0 C A:LEU240 3.5 34.3 1.0 CB A:ASP289 3.8 38.8 1.0 NE2 A:GLN348 3.8 36.5 1.0 CB A:ASP238 4.1 35.7 1.0 CA A:ASP238 4.1 35.4 1.0 OD2 A:ASP238 4.3 33.9 1.0 N A:LEU240 4.3 35.1 1.0 N A:GLY241 4.4 34.6 1.0 CA A:LEU240 4.4 34.8 1.0 OD1 A:ASP289 4.5 37.9 1.0 CB A:ASP287 4.5 42.6 1.0 CA A:GLY241 4.5 33.3 1.0 C A:ASP238 4.6 34.4 1.0 N A:ASP289 4.6 38.1 1.0 CG A:PRO299 4.6 45.3 1.0 CG A:GLN348 4.8 36.5 1.0 N A:ASP239 4.8 34.6 1.0 CA A:ASP289 4.8 40.0 1.0 CB A:LEU240 4.9 35.5 1.0 C A:GLY241 4.9 34.1 1.0 CD A:PRO299 5.0 45.7 1.0 O A:GLY241 5.0 35.2 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:37.2 occ:1.00 OD1 B:ASP236 2.2 35.3 1.0 OD1 B:ASP289 2.3 41.1 1.0 OD1 B:ASP239 2.4 38.5 1.0 O B:GLY237 2.5 36.7 1.0 OE1 B:GLU137 2.6 38.5 1.0 O B:HOH1123 2.6 35.7 1.0 CG B:ASP289 3.2 37.9 1.0 CD B:GLU137 3.3 40.2 1.0 CG B:ASP236 3.4 37.1 1.0 OE2 B:GLU137 3.5 41.3 1.0 CG B:ASP239 3.7 40.1 1.0 C B:GLY237 3.7 38.3 1.0 OD2 B:ASP289 3.8 36.1 1.0 N B:GLY237 3.9 40.1 1.0 CB B:ASP289 4.0 38.8 1.0 OD2 B:ASP236 4.0 39.1 1.0 N B:ASP239 4.3 38.0 1.0 CA B:GLY237 4.4 39.6 1.0 OD2 B:ASP239 4.4 43.9 1.0 CD1 B:LEU240 4.5 34.6 1.0 CB B:TYR201 4.5 43.3 1.0 CG B:LEU240 4.5 35.5 1.0 CA B:ASP289 4.6 40.7 1.0 CB B:ASP236 4.6 37.0 1.0 C B:ASP236 4.6 34.8 1.0 CG B:GLU137 4.7 42.4 1.0 CA B:ASP236 4.7 35.9 1.0 CB B:ASP239 4.7 38.6 1.0 N B:ASP238 4.8 38.1 1.0 N B:LEU240 4.8 34.3 1.0 CA B:ASP239 4.9 37.6 1.0 O B:HOH1110 4.9 26.8 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:38.5 occ:1.00 O B:LEU240 2.2 32.4 1.0 OD1 B:ASP238 2.3 33.1 1.0 OE1 B:GLN348 2.4 31.9 1.0 OD1 B:ASP287 2.4 37.4 1.0 O B:HOH1104 2.4 40.0 1.0 OD2 B:ASP289 2.5 36.1 1.0 OD2 B:ASP287 2.8 39.0 1.0 CG B:ASP287 2.9 36.7 1.0 CD B:GLN348 3.4 32.9 1.0 CG B:ASP289 3.4 37.9 1.0 C B:LEU240 3.4 33.3 1.0 CG B:ASP238 3.4 34.8 1.0 CB B:ASP289 3.7 38.8 1.0 NE2 B:GLN348 3.8 30.4 1.0 CB B:ASP238 4.2 36.5 1.0 CA B:ASP238 4.2 36.3 1.0 O B:HOH1118 4.2 33.8 1.0 N B:LEU240 4.3 34.3 1.0 N B:GLY241 4.3 33.2 1.0 CA B:LEU240 4.4 33.7 1.0 OD2 B:ASP238 4.4 33.0 1.0 CB B:ASP287 4.4 36.3 1.0 CA B:GLY241 4.4 31.9 1.0 OD1 B:ASP289 4.5 41.1 1.0 N B:ASP289 4.5 39.9 1.0 CG B:PRO299 4.7 43.7 1.0 C B:ASP238 4.7 36.5 1.0 CG B:GLN348 4.7 34.3 1.0 CA B:ASP289 4.8 40.7 1.0 C B:GLY241 4.8 31.3 1.0 N B:ASP239 4.8 38.0 1.0 CB B:LEU240 4.9 34.3 1.0 O B:GLY241 4.9 31.5 1.0 CD B:PRO299 5.0 44.9 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1001 b:43.5 occ:1.00 OD1 C:ASP236 2.2 40.3 1.0 O C:HOH1126 2.3 34.3 1.0 OE2 C:GLU137 2.3 45.3 1.0 OD1 C:ASP239 2.3 44.6 1.0 O C:GLY237 2.4 38.1 1.0 OD1 C:ASP289 2.4 44.6 1.0 CD C:GLU137 3.2 46.1 1.0 CG C:ASP289 3.3 42.7 1.0 CG C:ASP236 3.5 41.8 1.0 C C:GLY237 3.5 38.7 1.0 OE1 C:GLU137 3.6 48.7 1.0 CG C:ASP239 3.6 45.1 1.0 N C:GLY237 3.8 40.4 1.0 OD2 C:ASP289 3.9 41.9 1.0 O C:HOH1105 3.9 49.6 1.0 OD2 C:ASP236 4.1 43.1 1.0 CB C:ASP289 4.2 41.0 1.0 N C:ASP239 4.2 40.2 1.0 CA C:GLY237 4.2 40.0 1.0 OD2 C:ASP239 4.3 48.5 1.0 CG C:GLU137 4.5 45.5 1.0 C C:ASP236 4.5 40.4 1.0 CB C:TYR201 4.5 42.4 1.0 CB C:ASP239 4.6 43.9 1.0 CD1 C:LEU240 4.6 35.3 1.0 CA C:ASP236 4.6 40.4 1.0 CB C:ASP236 4.6 41.3 1.0 N C:ASP238 4.6 39.0 1.0 CG C:LEU240 4.7 35.3 1.0 CA C:ASP289 4.7 39.9 1.0 CA C:ASP239 4.8 41.9 1.0 N C:LEU240 4.9 37.9 1.0 CA C:ASP238 5.0 38.9 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:39.3 occ:1.00 OD1 C:ASP238 2.1 39.8 1.0 OE1 C:GLN348 2.3 34.3 1.0 O C:HOH1103 2.3 47.7 1.0 O C:LEU240 2.4 33.2 1.0 OD1 C:ASP287 2.5 42.1 1.0 OD2 C:ASP289 2.6 41.9 1.0 OD2 C:ASP287 2.9 39.5 1.0 CG C:ASP287 3.0 41.0 1.0 CG C:ASP238 3.2 39.5 1.0 CD C:GLN348 3.3 36.1 1.0 CG C:ASP289 3.5 42.7 1.0 C C:LEU240 3.6 34.4 1.0 NE2 C:GLN348 3.7 35.7 1.0 CB C:ASP289 3.8 41.0 1.0 CB C:ASP238 4.0 38.5 1.0 OD2 C:ASP238 4.1 41.3 1.0 CA C:ASP238 4.1 38.9 1.0 N C:LEU240 4.4 37.9 1.0 CG C:PRO299 4.5 41.4 1.0 N C:GLY241 4.5 33.3 1.0 CB C:ASP287 4.5 39.5 1.0 CA C:LEU240 4.5 35.6 1.0 CA C:GLY241 4.6 32.6 1.0 C C:ASP238 4.6 40.3 1.0 OD1 C:ASP289 4.6 44.6 1.0 CG C:GLN348 4.7 37.2 1.0 N C:ASP289 4.7 38.0 1.0 O C:HOH1121 4.7 31.9 1.0 N C:ASP239 4.8 40.2 1.0 CD C:PRO299 4.9 41.9 1.0 CA C:ASP289 4.9 39.9 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Protocadherin-15 EC2-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:39.8 occ:1.00 OD1 D:ASP236 2.2 40.7 1.0 O D:GLY237 2.4 39.0 1.0 OE1 D:GLU137 2.4 50.6 1.0 OD1 D:ASP239 2.4 41.6 1.0 OD1 D:ASP289 2.5 42.2 1.0 O D:HOH1109 2.6 41.0 1.0 CD D:GLU137 3.2 50.4 1.0 CG D:ASP289 3.3 41.7 1.0 CG D:ASP236 3.4 42.3 1.0 OE2 D:GLU137 3.4 49.8 1.0 C D:GLY237 3.5 40.2 1.0 CG D:ASP239 3.6 44.4 1.0 N D:GLY237 3.7 39.9 1.0 OD2 D:ASP289 3.9 40.5 1.0 OD2 D:ASP236 4.1 42.0 1.0 CA D:GLY237 4.2 40.8 1.0 CB D:ASP289 4.2 41.7 1.0 N D:ASP239 4.3 42.2 1.0 OD2 D:ASP239 4.4 49.2 1.0 CB D:TYR201 4.4 44.5 1.0 C D:ASP236 4.5 44.5 1.0 CG D:GLU137 4.5 50.8 1.0 CA D:ASP236 4.5 44.9 1.0 CB D:ASP236 4.6 44.1 1.0 CB D:ASP239 4.7 43.3 1.0 N D:ASP238 4.7 42.1 1.0 CD1 D:LEU240 4.7 36.0 1.0 CG D:LEU240 4.7 36.0 1.0 CA D:ASP289 4.7 43.5 1.0 CA D:ASP239 4.9 41.8 1.0 N D:LEU240 5.0 37.1 1.0 O D:HOH1114 5.0 38.4 1.0 CA D:ASP238 5.0 41.1 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Human Protocadherin-15 EC2-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Protocadherin-15 EC2-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1002 b:39.5 occ:1.00 O D:HOH1102 2.2 53.7 1.0 OD1 D:ASP238 2.2 41.7 1.0 O D:LEU240 2.3 33.1 1.0 OE1 D:GLN348 2.4 45.0 1.0 OD1 D:ASP287 2.5 39.9 1.0 OD2 D:ASP289 2.5 40.5 1.0 OD2 D:ASP287 2.9 43.5 1.0 CG D:ASP287 3.0 41.1 1.0 CG D:ASP238 3.3 41.7 1.0 CD D:GLN348 3.4 45.1 1.0 CG D:ASP289 3.4 41.7 1.0 C D:LEU240 3.5 34.0 1.0 CB D:ASP289 3.7 41.7 1.0 NE2 D:GLN348 3.7 44.5 1.0 CB D:ASP238 4.0 41.6 1.0 CA D:ASP238 4.1 41.1 1.0 OD2 D:ASP238 4.2 44.4 1.0 CD1 D:ILE292 4.2 49.2 1.0 N D:LEU240 4.3 37.1 1.0 CA D:LEU240 4.5 35.5 1.0 N D:GLY241 4.5 33.2 1.0 OD1 D:ASP289 4.5 42.2 1.0 CB D:ASP287 4.5 40.1 1.0 CA D:GLY241 4.6 32.7 1.0 C D:ASP238 4.6 42.3 1.0 N D:ASP289 4.6 42.3 1.0 CG D:PRO299 4.6 42.3 1.0 CG D:GLN348 4.7 44.8 1.0 CA D:ASP289 4.8 43.5 1.0 N D:ASP239 4.8 42.2 1.0 CD D:PRO299 4.9 43.5 1.0 CB D:LEU240 5.0 35.5 1.0

L.N.Wimalasena, M.Sotomayor. Structure of Inner-Ear Protocadherin-15 Fragment EC2-3 To Be Published.