Calcium in PDB 6n2e: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E

The structure of Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E, PDB code: 6n2e was solved by D.Choudhary, P.De-La-Torre, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.792, 65.397, 190.015, 90.00, 99.12, 90.00
R / Rfree (%)	22.5 / 25.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E (pdb code 6n2e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E, PDB code: 6n2e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.4 occ:1.00 OD1 A:ASP83 2.1 92.5 1.0 OE2 A:GLU28 2.1 92.4 1.0 OD2 A:ASP85 2.2 89.2 1.0 OD2 A:ASP121 2.6 88.8 1.0 CG A:ASP83 3.1 93.7 1.0 OE1 A:GLU27 3.2 90.4 1.0 CG A:ASP85 3.2 88.9 1.0 CD A:GLU28 3.4 93.4 1.0 CG A:ASP121 3.5 87.1 1.0 OD2 A:ASP83 3.6 94.3 1.0 CB A:ASP85 3.7 89.5 1.0 OD1 A:ASP121 3.7 85.9 1.0 ND2 A:ASN122 3.8 84.2 1.0 OE1 A:GLU28 4.1 94.3 1.0 CB A:ASP83 4.2 94.5 1.0 CA A:CA402 4.2 89.7 1.0 N A:ASP85 4.2 90.3 1.0 OD1 A:ASP85 4.3 88.4 1.0 CG A:GLU28 4.3 93.8 1.0 CD A:GLU27 4.4 90.1 1.0 CA A:ASP83 4.4 93.9 1.0 CA A:ASP85 4.6 90.0 1.0 N A:ARG84 4.6 91.8 1.0 CG A:ASN122 4.8 82.8 1.0 C A:ASP83 4.9 93.0 1.0 OE2 A:GLU27 4.9 89.5 1.0 CB A:ASP121 4.9 86.8 1.0 OD1 A:ASN122 4.9 83.8 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:89.7 occ:1.00 OD1 A:ASP118 2.3 87.9 1.0 OD1 A:ASP85 2.3 88.4 1.0 O A:ARG119 2.3 88.6 1.0 OD1 A:ASP159 2.3 84.2 1.0 OD1 A:ASP121 2.4 85.9 1.0 OE2 A:GLU27 2.4 89.5 1.0 OD2 A:ASP85 2.5 89.2 1.0 CG A:ASP85 2.8 88.9 1.0 CD A:GLU27 3.2 90.1 1.0 CG A:ASP159 3.2 82.6 1.0 OE1 A:GLU27 3.3 90.4 1.0 CG A:ASP118 3.4 88.0 1.0 C A:ARG119 3.5 88.9 1.0 CG A:ASP121 3.5 87.1 1.0 N A:ARG119 3.8 89.5 1.0 ND2 A:ASN122 3.9 84.2 1.0 CB A:ASP159 4.0 82.0 1.0 OD2 A:ASP118 4.0 87.6 1.0 OD2 A:ASP121 4.1 88.8 1.0 OD2 A:ASP159 4.1 81.6 1.0 N A:ASP121 4.1 83.5 1.0 CA A:ARG119 4.2 89.6 1.0 CA A:ASP159 4.2 82.6 1.0 CA A:CA401 4.2 0.4 1.0 CB A:ASP85 4.3 89.5 1.0 N A:ASN120 4.5 84.5 1.0 CB A:ASP118 4.6 88.7 1.0 CB A:ARG119 4.7 90.5 1.0 CA A:ASP118 4.7 89.4 1.0 CG A:GLU27 4.7 91.0 1.0 C A:ASP118 4.7 89.5 1.0 CB A:ASP121 4.7 86.8 1.0 CA A:ASN120 4.8 82.4 1.0 CA A:ASP121 4.9 84.4 1.0 C A:ASN120 5.0 82.7 1.0 N A:ASP85 5.0 90.3 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:76.2 occ:1.00 OD1 A:ASN120 2.2 78.3 1.0 O A:ASN163 2.2 78.7 1.0 O A:ASN122 2.3 77.4 1.0 OD2 A:ASP157 2.4 75.2 1.0 OD2 A:ASP215 2.6 76.0 1.0 OD2 A:ASP159 2.6 81.6 1.0 OD1 A:ASP157 2.6 77.5 1.0 CG A:ASP157 2.8 75.7 1.0 CG A:ASN120 3.3 79.2 1.0 C A:ASN163 3.4 79.6 1.0 CG A:ASP215 3.4 75.5 1.0 CG A:ASP159 3.5 82.6 1.0 C A:ASN122 3.5 77.9 1.0 CB A:ASP215 3.7 74.3 1.0 CB A:ASP159 3.7 82.0 1.0 ND2 A:ASN120 3.9 78.6 1.0 CA A:ASN163 4.1 81.2 1.0 CB A:ASN163 4.2 83.1 1.0 CB A:ASP157 4.3 74.4 1.0 CA A:ASN122 4.4 80.0 1.0 N A:GLY164 4.4 79.6 1.0 N A:ASN122 4.4 81.3 1.0 N A:SER123 4.5 77.1 1.0 OD1 A:ASP215 4.5 76.1 1.0 CD A:ARG224 4.5 80.8 1.0 CB A:ASN120 4.5 81.5 1.0 CA A:GLY164 4.6 78.4 1.0 CA A:ASN120 4.7 82.4 1.0 CA A:SER123 4.7 75.2 1.0 CB A:ASN122 4.7 80.3 1.0 OD1 A:ASP159 4.7 84.2 1.0 C A:SER123 4.9 73.9 1.0 C A:ASN120 4.9 82.7 1.0 CA A:ASP159 4.9 82.6 1.0 N A:ASP159 4.9 81.2 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:38.9 occ:1.00 OD1 A:ASP236 2.2 41.5 1.0 OD1 A:ASP289 2.3 42.1 1.0 OE2 A:GLU137 2.3 41.2 1.0 OD1 A:ASP239 2.5 42.2 1.0 O A:GLY237 2.5 39.9 1.0 O A:HOH513 2.6 41.2 1.0 CG A:ASP289 3.3 42.2 1.0 CD A:GLU137 3.4 41.2 1.0 CG A:ASP236 3.4 42.4 1.0 CG A:ASP239 3.6 42.7 1.0 N A:GLY237 3.7 40.6 1.0 C A:GLY237 3.7 40.1 1.0 OE1 A:GLU137 3.8 41.5 1.0 CB A:ASP289 4.0 42.5 1.0 OD2 A:ASP236 4.1 43.2 1.0 OD2 A:ASP289 4.1 42.3 1.0 OD2 A:ASP239 4.3 43.1 1.0 N A:ASP239 4.3 42.7 1.0 CA A:GLY237 4.4 40.4 1.0 CA A:ASP236 4.4 41.8 1.0 C A:ASP236 4.4 41.3 1.0 CB A:TYR201 4.4 43.6 1.0 CD1 A:LEU240 4.5 40.3 1.0 CB A:ASP236 4.5 42.8 1.0 CG A:LEU240 4.6 40.5 1.0 O A:HOH502 4.6 45.4 1.0 CB A:ASP239 4.6 43.3 1.0 CA A:ASP289 4.6 42.3 1.0 CG A:GLU137 4.7 41.2 1.0 OE2 A:GLU202 4.7 47.4 1.0 N A:ASP238 4.8 40.2 1.0 CA A:ASP239 4.9 42.9 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:39.5 occ:1.00 OD2 A:ASP289 2.2 42.3 1.0 OE1 A:GLN348 2.2 41.4 1.0 OD1 A:ASP238 2.3 40.4 1.0 O A:LEU240 2.5 40.7 1.0 OD1 A:ASP287 2.6 41.1 1.0 OD2 A:ASP287 2.8 42.3 1.0 CG A:ASP287 3.0 41.6 1.0 CD A:GLN348 3.2 41.9 1.0 CG A:ASP289 3.3 42.2 1.0 CG A:ASP238 3.4 40.7 1.0 NE2 A:GLN348 3.6 42.8 1.0 C A:LEU240 3.7 40.4 1.0 CB A:ASP289 3.8 42.5 1.0 CA A:ASP238 3.9 40.1 1.0 CB A:ASP238 4.1 40.7 1.0 N A:LEU240 4.3 41.3 1.0 OD2 A:ASP238 4.4 41.2 1.0 C A:ASP238 4.4 39.7 1.0 OD1 A:ASP289 4.4 42.1 1.0 CB A:ASP287 4.5 41.7 1.0 CG A:GLN348 4.6 41.9 1.0 CA A:LEU240 4.6 40.7 1.0 CG A:PRO299 4.6 45.8 1.0 N A:ASP239 4.6 42.7 1.0 N A:ASP289 4.6 41.4 1.0 N A:GLY241 4.7 40.3 1.0 CA A:ASP289 4.8 42.3 1.0 CA A:GLY241 4.9 40.2 1.0 O A:ASP238 4.9 39.9 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:65.0 occ:1.00 OE2 B:GLU28 2.2 59.7 1.0 OD2 B:ASP85 2.2 60.9 1.0 OE2 B:GLU27 2.2 58.7 1.0 OD2 B:ASP121 2.4 59.3 1.0 O B:HOH518 2.4 58.4 1.0 OD1 B:ASP83 2.5 63.1 1.0 CG B:ASP121 3.2 58.5 1.0 CG B:ASP85 3.2 62.2 1.0 CD B:GLU27 3.3 58.1 1.0 OD1 B:ASP121 3.4 58.5 1.0 CD B:GLU28 3.4 59.2 1.0 CG B:ASP83 3.4 64.1 1.0 CB B:ASP85 3.7 63.9 1.0 OE1 B:GLU27 3.8 58.4 1.0 OD2 B:ASP83 4.0 65.4 1.0 N B:ASP85 4.1 63.8 1.0 CA B:CA402 4.1 58.1 1.0 CG B:GLU28 4.1 58.6 1.0 OD1 B:ASN122 4.3 58.6 1.0 OD1 B:ASP85 4.3 62.3 1.0 OE1 B:GLU28 4.3 59.5 1.0 N B:ARG84 4.4 62.1 1.0 CB B:ASP83 4.4 64.0 1.0 CA B:ASP83 4.4 62.7 1.0 CA B:ASP85 4.5 65.0 1.0 CG B:GLU27 4.6 57.4 1.0 CB B:ASP121 4.6 57.7 1.0 C B:ASP83 4.8 63.1 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:58.1 occ:1.00 OD1 B:ASP118 2.1 59.2 1.0 OE1 B:GLU27 2.3 58.4 1.0 OD1 B:ASP159 2.4 59.0 1.0 O B:ARG119 2.5 57.1 1.0 OD1 B:ASP85 2.5 62.3 1.0 OD1 B:ASP121 2.5 58.5 1.0 OD2 B:ASP85 2.5 60.9 1.0 CG B:ASP85 2.8 62.2 1.0 CG B:ASP118 3.2 59.6 1.0 CG B:ASP159 3.3 58.4 1.0 CD B:GLU27 3.3 58.1 1.0 CG B:ASP121 3.7 58.5 1.0 C B:ARG119 3.7 56.4 1.0 OE2 B:GLU27 3.7 58.7 1.0 N B:ARG119 3.7 56.7 1.0 OD2 B:ASP118 3.8 60.2 1.0 CB B:ASP159 3.9 59.0 1.0 CA B:CA401 4.1 65.0 1.0 OD2 B:ASP159 4.2 57.3 1.0 CA B:ASP159 4.2 60.1 1.0 CA B:ARG119 4.3 56.0 1.0 N B:ASP121 4.3 56.8 1.0 OD2 B:ASP121 4.3 59.3 1.0 CB B:ASP85 4.3 63.9 1.0 CB B:ASP118 4.4 59.6 1.0 OD1 B:ASN122 4.5 58.6 1.0 CA B:ASP118 4.5 58.3 1.0 C B:ASP118 4.6 57.3 1.0 CG B:GLU27 4.7 57.4 1.0 N B:ASN120 4.8 58.0 1.0 CB B:ASP121 4.8 57.7 1.0 CB B:ARG119 4.9 55.3 1.0 CA B:ASN120 5.0 57.0 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


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 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:60.5 occ:1.00 OD1 B:ASN120 2.2 55.8 1.0 O B:ASN122 2.3 54.9 1.0 O B:ASN163 2.3 58.4 1.0 OD2 B:ASP159 2.4 57.3 1.0 OD2 B:ASP215 2.5 55.9 1.0 OD2 B:ASP157 2.6 54.9 1.0 OD1 B:ASP157 2.7 56.6 1.0 CG B:ASP157 3.0 55.7 1.0 CG B:ASN120 3.2 55.9 1.0 CG B:ASP159 3.4 58.4 1.0 CG B:ASP215 3.4 55.9 1.0 C B:ASN122 3.5 55.1 1.0 C B:ASN163 3.5 59.4 1.0 CB B:ASP159 3.7 59.0 1.0 ND2 B:ASN120 3.7 55.4 1.0 CB B:ASP215 3.9 56.0 1.0 N B:ASN122 4.2 56.2 1.0 CA B:ASN163 4.2 60.0 1.0 CA B:ASN122 4.3 56.0 1.0 CB B:ASN163 4.3 60.4 1.0 CB B:ASP157 4.4 55.8 1.0 OD1 B:ASP215 4.4 56.2 1.0 CB B:ASN120 4.5 56.8 1.0 N B:SER123 4.5 54.9 1.0 CB B:ASN122 4.5 56.8 1.0 CA B:ASN120 4.5 57.0 1.0 N B:GLY164 4.5 60.3 1.0 OD1 B:ASP159 4.5 59.0 1.0 C B:ASN120 4.6 56.4 1.0 O B:ASN120 4.6 55.9 1.0 CG B:ARG224 4.7 56.2 1.0 CA B:GLY164 4.8 59.9 1.0 CA B:SER123 4.8 54.2 1.0 CA B:ASP159 4.9 60.1 1.0 N B:ASP159 4.9 59.6 1.0 N B:ASP121 5.0 56.8 1.0 CB B:ARG224 5.0 55.6 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:42.2 occ:1.00 OE1 B:GLN348 2.2 41.1 1.0 OD1 B:ASP238 2.2 41.5 1.0 O B:LEU240 2.3 41.9 1.0 OD2 B:ASP289 2.4 46.4 1.0 OD1 B:ASP287 2.5 43.2 1.0 OD2 B:ASP287 2.7 44.3 1.0 CG B:ASP287 2.9 43.7 1.0 CD B:GLN348 3.3 40.6 1.0 CG B:ASP238 3.4 41.4 1.0 CG B:ASP289 3.4 47.4 1.0 C B:LEU240 3.5 41.6 1.0 NE2 B:GLN348 3.7 41.0 1.0 CB B:ASP289 3.8 47.9 1.0 CA B:ASP238 4.1 41.6 1.0 N B:LEU240 4.2 43.5 1.0 CB B:ASP238 4.3 41.5 1.0 OD2 B:ASP238 4.3 41.2 1.0 CB B:ASP287 4.3 43.7 1.0 N B:GLY241 4.4 40.8 1.0 CA B:LEU240 4.4 42.5 1.0 CA B:GLY241 4.5 40.1 1.0 CG B:PRO299 4.5 45.8 1.0 N B:ASP289 4.6 46.5 1.0 OD1 B:ASP289 4.6 48.0 1.0 CG B:GLN348 4.6 39.9 1.0 C B:ASP238 4.6 41.4 1.0 CA B:ASP289 4.8 48.2 1.0 CD B:PRO299 4.9 47.2 1.0 CB B:LEU240 4.9 43.1 1.0 N B:ASP239 5.0 46.0 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:44.3 occ:1.00 OE2 B:GLU137 2.1 44.2 1.0 O B:HOH513 2.1 48.8 1.0 OD1 B:ASP239 2.2 47.5 1.0 OD1 B:ASP289 2.3 48.0 1.0 OD1 B:ASP236 2.3 46.3 1.0 O B:GLY237 2.3 42.8 1.0 CD B:GLU137 3.2 44.2 1.0 CG B:ASP239 3.3 47.5 1.0 CG B:ASP289 3.3 47.4 1.0 C B:GLY237 3.5 42.5 1.0 N B:GLY237 3.5 43.8 1.0 CG B:ASP236 3.5 47.0 1.0 OE1 B:GLU137 3.8 44.9 1.0 OD2 B:ASP239 3.9 48.4 1.0 CA B:GLY237 4.0 42.9 1.0 N B:ASP239 4.1 46.0 1.0 OD2 B:ASP289 4.1 46.4 1.0 CB B:ASP289 4.2 47.9 1.0 C B:ASP236 4.3 44.7 1.0 OD2 B:ASP236 4.3 48.3 1.0 CG B:GLU137 4.3 43.6 1.0 CB B:ASP239 4.4 47.1 1.0 CA B:ASP236 4.4 45.9 1.0 CB B:ASP236 4.5 47.0 1.0 N B:ASP238 4.6 42.0 1.0 CB B:TYR201 4.6 48.4 1.0 CG B:LEU240 4.6 44.4 1.0 CA B:ASP239 4.7 45.6 1.0 O B:HOH507 4.8 51.0 1.0 CD1 B:LEU240 4.8 45.2 1.0 CA B:ASP289 4.8 48.2 1.0 N B:LEU240 4.8 43.5 1.0 CA B:ASP238 5.0 41.6 1.0

D.Choudhary, P.De-La-Torre, M.Sotomayor. Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E To Be Published.