Calcium in PDB 6mfo: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N

The structure of Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N, PDB code: 6mfo 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)	49.99 / 3.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.894, 116.516, 99.889, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 28.8

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

Calcium binding site 1 out of 5 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:50.2 occ:1.00 OD1 A:ASP83 2.1 61.6 1.0 OE1 A:GLU27 2.3 45.3 1.0 O A:HOH501 2.3 37.6 1.0 OD2 A:ASP85 2.3 66.8 1.0 OD2 A:ASP121 2.4 67.2 1.0 OE1 A:GLU28 2.5 63.0 1.0 CG A:ASP121 3.1 62.8 1.0 OD1 A:ASP121 3.2 62.6 1.0 CD A:GLU27 3.2 46.8 1.0 CD A:GLU28 3.3 62.0 1.0 CG A:ASP85 3.4 65.2 1.0 CG A:ASP83 3.4 59.7 1.0 OE2 A:GLU27 3.5 47.4 1.0 CG A:GLU28 3.6 61.0 1.0 CA A:CA402 3.7 56.8 1.0 CB A:ASP85 3.9 63.2 1.0 ND2 A:ASN122 3.9 56.1 1.0 CA A:ASP83 4.1 60.2 1.0 CB A:ASP83 4.2 59.4 1.0 OD2 A:ASP83 4.3 58.8 1.0 N A:ASP85 4.3 59.5 1.0 N A:ARG84 4.3 60.7 1.0 OD1 A:ASP85 4.4 68.1 1.0 OE2 A:GLU28 4.4 62.6 1.0 CG A:GLU27 4.5 47.5 1.0 C A:ASP83 4.5 61.1 1.0 CB A:ASP121 4.6 60.2 1.0 CA A:ASP85 4.7 63.1 1.0 O A:HOH505 5.0 50.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:56.8 occ:1.00 OD1 A:ASP118 2.2 59.5 1.0 OD1 A:ASP121 2.3 62.6 1.0 OD1 A:ASP159 2.3 57.3 1.0 OD2 A:ASP85 2.3 66.8 1.0 OE2 A:GLU27 2.3 47.4 1.0 O A:ARG119 2.4 49.1 1.0 OD1 A:ASP85 2.6 68.1 1.0 CG A:ASP85 2.8 65.2 1.0 CG A:ASP159 3.2 57.6 1.0 CD A:GLU27 3.3 46.8 1.0 CG A:ASP118 3.4 58.4 1.0 CG A:ASP121 3.4 62.8 1.0 C A:ARG119 3.5 50.9 1.0 N A:ARG119 3.6 53.1 1.0 ND2 A:ASN122 3.6 56.1 1.0 CA A:CA401 3.7 50.2 1.0 OE1 A:GLU27 3.8 45.3 1.0 OD2 A:ASP159 4.0 55.1 1.0 OD2 A:ASP118 4.0 58.9 1.0 CB A:ASP159 4.0 59.9 1.0 OD2 A:ASP121 4.1 67.2 1.0 CA A:ARG119 4.1 52.6 1.0 N A:ASP121 4.2 56.2 1.0 CB A:ASP85 4.3 63.2 1.0 CA A:ASP159 4.3 62.1 1.0 O A:HOH502 4.4 35.1 1.0 CB A:ASP118 4.5 57.5 1.0 N A:ASN120 4.5 52.3 1.0 C A:ASP118 4.6 54.3 1.0 CA A:ASP118 4.6 56.0 1.0 CG A:GLU27 4.6 47.5 1.0 CB A:ASP121 4.6 60.2 1.0 O A:HOH501 4.7 37.6 1.0 CB A:ARG119 4.8 52.9 1.0 CG A:ASN122 4.8 56.4 1.0 CA A:ASN120 4.9 54.4 1.0 CA A:ASP121 4.9 56.8 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:58.5 occ:1.00 O A:ASN122 2.2 54.0 1.0 OD1 A:ASP157 2.2 58.7 1.0 OD1 A:ASN120 2.3 55.0 1.0 O A:ASN163 2.4 67.6 1.0 OD2 A:ASP157 2.5 56.2 1.0 OD2 A:ASP215 2.5 58.4 1.0 OD2 A:ASP159 2.5 55.1 1.0 CG A:ASP157 2.6 60.5 1.0 C A:ASN122 3.4 54.1 1.0 CG A:ASP159 3.4 57.6 1.0 CG A:ASP215 3.4 61.8 1.0 CG A:ASN120 3.5 54.1 1.0 C A:ASN163 3.6 63.6 1.0 CB A:ASP159 3.6 59.9 1.0 CB A:ASP215 3.8 62.7 1.0 CB A:ASP157 4.1 62.9 1.0 ND2 A:ASN120 4.2 54.0 1.0 CA A:ASN122 4.2 55.5 1.0 N A:SER123 4.3 57.3 1.0 N A:ASN122 4.3 55.1 1.0 CA A:ASN163 4.4 62.9 1.0 CA A:SER123 4.4 60.5 1.0 OD1 A:ASP159 4.5 57.3 1.0 OD1 A:ASP215 4.5 60.6 1.0 CA A:ASN120 4.5 54.4 1.0 CB A:ASN122 4.5 56.2 1.0 CB A:ASN163 4.5 62.1 1.0 CB A:ASN120 4.6 54.2 1.0 N A:GLY164 4.6 63.4 1.0 C A:ASN120 4.6 56.7 1.0 C A:SER123 4.7 63.6 1.0 CG A:ARG224 4.7 61.5 1.0 N A:ASP159 4.8 62.2 1.0 CA A:ASP159 4.8 62.1 1.0 CA A:GLY164 4.8 61.9 1.0 O A:ASN120 4.8 59.6 1.0 CD A:PRO124 4.8 67.5 1.0 N A:PRO124 5.0 66.6 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:67.0 occ:1.00 OD1 A:ASP238 2.1 59.7 1.0 O A:LEU240 2.4 60.9 1.0 OD2 A:ASP289 2.4 70.2 1.0 OD1 A:ASP287 2.5 66.3 1.0 OE1 A:GLN348 2.5 58.9 1.0 OD2 A:ASP287 3.1 67.2 1.0 CG A:ASP287 3.1 68.9 1.0 CG A:ASP238 3.1 59.5 1.0 CD A:GLN348 3.5 62.1 1.0 CG A:ASP289 3.5 72.4 1.0 C A:LEU240 3.6 56.7 1.0 CB A:ASP238 3.6 59.6 1.0 NE2 A:GLN348 3.6 56.7 1.0 CA A:ASP238 3.7 61.3 1.0 CB A:ASP289 4.0 74.6 1.0 N A:LEU240 4.0 57.2 1.0 OD2 A:ASP238 4.1 58.0 1.0 C A:ASP238 4.2 65.3 1.0 CA A:LEU240 4.4 57.4 1.0 N A:ASP239 4.4 67.3 1.0 CB A:ASP287 4.5 68.5 1.0 N A:ASP289 4.5 76.8 1.0 N A:GLY241 4.6 58.4 1.0 OD1 A:ASP289 4.6 70.2 1.0 CA A:GLY241 4.7 59.3 1.0 CG A:GLN348 4.9 65.5 1.0 CA A:ASP289 4.9 78.1 1.0 N A:ASP238 4.9 60.6 1.0 CB A:LEU240 4.9 58.4 1.0 CD1 A:ILE292 4.9 70.2 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:56.4 occ:1.00 OD1 A:ASP289 2.0 70.2 1.0 OD1 A:ASP236 2.2 68.5 1.0 OE2 A:GLU137 2.3 67.0 1.0 OD1 A:ASP239 2.4 70.2 1.0 O A:GLY237 2.5 57.7 1.0 CG A:ASP289 3.1 72.4 1.0 CG A:ASP239 3.3 68.0 1.0 CG A:ASP236 3.4 66.3 1.0 CD A:GLU137 3.5 64.9 1.0 C A:GLY237 3.6 60.7 1.0 OD2 A:ASP239 3.6 68.1 1.0 N A:GLY237 3.7 65.2 1.0 CB A:ASP289 3.8 74.6 1.0 OE1 A:GLU137 4.0 66.1 1.0 OD2 A:ASP289 4.1 70.2 1.0 OD2 A:ASP236 4.1 66.7 1.0 CA A:GLY237 4.2 63.2 1.0 C A:ASP236 4.3 63.6 1.0 N A:ASP239 4.4 67.3 1.0 CA A:ASP236 4.4 64.6 1.0 CA A:ASP289 4.5 78.1 1.0 CB A:ASP236 4.5 66.6 1.0 CD1 A:LEU240 4.5 62.3 1.0 CB A:ASP239 4.6 67.1 1.0 CG A:GLU137 4.7 62.3 1.0 N A:ASP238 4.7 60.6 1.0 CG A:LEU240 4.8 60.2 1.0

D.Choudhary, M.Sotomayor. Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N To Be Published.