Calcium in PDB 5cyx: Crystal Structure of Mouse Protocadherin-24 EC1-3

The structure of Crystal Structure of Mouse Protocadherin-24 EC1-3, PDB code: 5cyx was solved by Z.R.Johnson, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.767, 74.767, 140.620, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.7

The structure of Crystal Structure of Mouse Protocadherin-24 EC1-3 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-24 EC1-3 (pdb code 5cyx). 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 Mouse Protocadherin-24 EC1-3, PDB code: 5cyx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Mouse Protocadherin-24 EC1-3


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 Mouse Protocadherin-24 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:77.2 occ:1.00 OD2 A:ASP99 2.2 49.2 1.0 OD1 A:ASP66 2.3 53.7 1.0 OE1 A:GLU17 2.4 45.2 1.0 OE1 A:GLU68 2.4 50.8 1.0 O A:HOH1174 2.5 57.3 1.0 CG A:ASP99 3.2 48.1 1.0 CD A:GLU17 3.3 45.4 1.0 OD1 A:ASP99 3.4 46.3 1.0 CG A:ASP66 3.4 53.1 1.0 CD A:GLU68 3.6 50.4 1.0 OE2 A:GLU17 3.6 43.9 1.0 CA A:CA1002 4.0 42.8 1.0 CA A:ASP66 4.1 49.5 1.0 N A:PHE67 4.2 49.7 1.0 OD2 A:ASP66 4.2 56.8 1.0 ND2 A:ASN100 4.3 50.7 1.0 CB A:ASP66 4.3 52.0 1.0 N A:GLU68 4.4 50.2 1.0 CG A:GLU68 4.4 51.2 1.0 CB A:GLU68 4.5 52.1 1.0 OE2 A:GLU68 4.5 48.5 1.0 C A:ASP66 4.5 49.0 1.0 CG A:GLU17 4.5 45.5 1.0 CB A:ASP99 4.6 46.7 1.0 O A:HOH1189 4.6 63.6 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Mouse Protocadherin-24 EC1-3


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 Mouse Protocadherin-24 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:42.8 occ:1.00 OE2 A:GLU17 2.2 43.9 1.0 OD1 A:ASP96 2.3 46.9 1.0 OD1 A:ASP99 2.4 46.3 1.0 OD1 A:ASP132 2.4 42.2 1.0 O A:ARG97 2.4 42.9 1.0 OE2 A:GLU68 2.5 48.5 1.0 OE1 A:GLU68 2.7 50.8 1.0 CD A:GLU68 2.9 50.4 1.0 CD A:GLU17 3.3 45.4 1.0 CG A:ASP132 3.4 42.5 1.0 CG A:ASP99 3.4 48.1 1.0 CG A:ASP96 3.5 48.8 1.0 C A:ARG97 3.7 44.8 1.0 N A:ARG97 3.8 45.1 1.0 OE1 A:GLU17 3.8 45.2 1.0 OD2 A:ASP99 3.9 49.2 1.0 ND2 A:ASN100 4.0 50.7 1.0 CA A:CA1001 4.0 77.2 1.0 CB A:ASP132 4.0 42.2 1.0 N A:ASP99 4.2 45.1 1.0 OD2 A:ASP96 4.2 49.1 1.0 OD2 A:ASP132 4.3 41.6 1.0 CA A:ASP132 4.4 43.2 1.0 CA A:ARG97 4.4 45.7 1.0 CG A:GLU68 4.4 51.2 1.0 CG A:GLU17 4.6 45.5 1.0 CA A:ASP96 4.6 47.5 1.0 C A:ASP96 4.7 46.0 1.0 CB A:ASP96 4.7 47.6 1.0 CB A:PHE67 4.7 49.2 1.0 CB A:ASP99 4.7 46.7 1.0 N A:ASN98 4.7 42.8 1.0 N A:ASN100 4.8 49.5 1.0 CD2 A:PHE67 4.9 48.8 1.0 CA A:ASN98 4.9 43.4 1.0 O A:HOH1117 4.9 45.5 1.0 CA A:ASP99 4.9 46.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Mouse Protocadherin-24 EC1-3


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 Mouse Protocadherin-24 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:41.4 occ:1.00 OD1 A:ASN98 2.3 44.0 1.0 OD2 A:ASP130 2.3 47.6 1.0 O A:ASN100 2.3 45.3 1.0 O A:ALA136 2.3 43.0 1.0 OD2 A:ASP132 2.3 41.6 1.0 OD2 A:ASP188 2.5 49.3 1.0 OD1 A:ASP130 2.5 47.1 1.0 CG A:ASP130 2.8 47.9 1.0 C A:ASN100 3.4 49.0 1.0 CG A:ASP132 3.4 42.5 1.0 CG A:ASN98 3.4 42.9 1.0 CG A:ASP188 3.5 48.4 1.0 C A:ALA136 3.6 43.7 1.0 CB A:ASP132 3.8 42.2 1.0 CB A:ASP188 3.9 47.6 1.0 ND2 A:ASN98 4.0 42.2 1.0 N A:ASN100 4.1 49.5 1.0 CA A:ASN100 4.1 50.0 1.0 CB A:ASP130 4.3 48.1 1.0 CA A:ALA136 4.3 43.6 1.0 N A:ILE101 4.4 49.1 1.0 CG A:GLN200 4.4 49.5 1.0 CB A:ALA136 4.4 44.2 1.0 CB A:ASN100 4.5 50.1 1.0 CB A:GLN200 4.5 49.4 1.0 OD1 A:ASP132 4.5 42.2 1.0 N A:GLY137 4.6 43.8 1.0 OD1 A:ASP188 4.6 48.3 1.0 CA A:ILE101 4.6 49.9 1.0 CB A:ASN98 4.6 43.0 1.0 CA A:GLY137 4.7 44.5 1.0 CA A:ASN98 4.7 43.4 1.0 N A:ASP132 4.7 44.6 1.0 CA A:ASP132 4.9 43.2 1.0 C A:ASN98 4.9 44.8 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Mouse Protocadherin-24 EC1-3


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 Mouse Protocadherin-24 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:49.2 occ:1.00 OE2 A:GLU115 2.3 47.7 1.0 O A:GLU214 2.3 51.0 1.0 OD1 A:ASP213 2.3 45.8 1.0 OD1 A:ASP249 2.3 55.0 1.0 OD1 A:ASP216 2.4 58.9 1.0 O A:HOH1109 2.4 39.1 1.0 CD A:GLU115 3.3 46.9 1.0 CG A:ASP249 3.4 54.1 1.0 C A:GLU214 3.4 50.9 1.0 CG A:ASP216 3.5 58.7 1.0 CG A:ASP213 3.6 47.3 1.0 OE1 A:GLU115 3.6 46.3 1.0 N A:GLU214 3.7 49.0 1.0 OD1 A:ASN174 3.7 48.8 1.0 N A:ASP216 3.9 54.7 1.0 CB A:ASP249 4.0 53.5 1.0 OD2 A:ASP216 4.1 61.1 1.0 CA A:GLU214 4.1 50.9 1.0 OD2 A:ASP213 4.2 46.2 1.0 CD1 A:LEU217 4.3 64.3 1.0 OD2 A:ASP249 4.3 54.3 1.0 CG A:LEU217 4.4 64.4 1.0 N A:PRO215 4.5 52.2 1.0 C A:ASP213 4.5 48.7 1.0 CB A:ASP216 4.6 57.9 1.0 CG A:GLU115 4.6 46.1 1.0 CA A:PRO215 4.6 53.1 1.0 CA A:ASP213 4.6 47.5 1.0 CA A:ASP216 4.7 57.1 1.0 N A:LEU217 4.7 64.1 1.0 CB A:ASP213 4.7 47.7 1.0 CA A:ASP249 4.7 53.4 1.0 C A:PRO215 4.8 54.1 1.0 C A:ASP216 4.8 58.2 1.0 CB A:GLU214 4.8 51.4 1.0 CG A:ASN174 4.9 49.7 1.0 O A:HOH1102 4.9 46.0 1.0 CB A:LEU217 5.0 63.9 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Mouse Protocadherin-24 EC1-3


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 Mouse Protocadherin-24 EC1-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:55.5 occ:1.00 OD2 A:ASP249 2.2 54.3 1.0 O A:LEU217 2.3 61.0 1.0 OE1 A:GLU303 2.4 62.2 1.0 OD1 A:ASP247 2.4 57.3 1.0 OE2 A:GLU303 2.5 60.1 1.0 O A:HOH1114 2.5 41.6 1.0 O A:HOH1172 2.5 42.9 1.0 CD A:GLU303 2.8 59.9 1.0 CG A:ASP247 3.3 56.5 1.0 CG A:ASP249 3.4 54.1 1.0 C A:LEU217 3.6 64.2 1.0 OD2 A:ASP247 3.6 55.1 1.0 CB A:ASP249 4.0 53.5 1.0 O A:HOH1137 4.0 46.0 1.0 N A:LEU217 4.1 64.1 1.0 CG A:GLU303 4.3 60.2 1.0 OD1 A:ASP249 4.3 55.0 1.0 N A:ASP249 4.4 54.3 1.0 CA A:LEU217 4.4 64.0 1.0 CB A:ASP247 4.5 56.4 1.0 O A:HOH1104 4.5 48.9 1.0 O A:HOH1153 4.5 50.9 1.0 CA A:PRO215 4.5 53.1 1.0 N A:ASP218 4.5 64.8 1.0 CB A:ALA313 4.6 68.5 1.0 N A:ASP216 4.6 54.7 1.0 CB A:PRO215 4.6 54.1 1.0 CA A:ASP218 4.7 66.1 1.0 C A:PRO215 4.7 54.1 1.0 C A:ASP218 4.7 65.7 1.0 N A:SER248 4.7 57.0 1.0 CB A:LEU217 4.8 63.9 1.0 CA A:ASP247 4.8 57.2 1.0 CA A:ASP249 4.8 53.4 1.0 N A:PRO219 5.0 64.9 1.0 O A:ASP218 5.0 65.7 1.0

Z.R.Johnson, M.Sotomayor. Crystal Structure of Mouse Protocadherin-24 EC1-3 To Be Published.