Calcium in PDB 4xhz: Crystal Structure of Human Protocadherin-15 EC8-10

The structure of Crystal Structure of Human Protocadherin-15 EC8-10, PDB code: 4xhz was solved by R.Araya-Secchi, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	136.77 / 2.80
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.929, 157.929, 142.898, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 20

The structure of Crystal Structure of Human Protocadherin-15 EC8-10 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC8-10 (pdb code 4xhz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-15 EC8-10, PDB code: 4xhz:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human Protocadherin-15 EC8-10


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 EC8-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:85.2 occ:1.00 O A:TYR901 2.2 91.2 1.0 OD2 A:ASP933 2.3 95.3 1.0 OD2 A:ASP989 2.3 82.2 1.0 OD1 A:ASN899 2.4 86.8 1.0 OD2 A:ASP931 2.4 92.8 1.0 O A:ALA939 2.5 77.6 1.0 OD1 A:ASP931 2.5 94.9 1.0 CG A:ASP931 2.8 89.2 1.0 CG A:ASP933 3.4 84.7 1.0 C A:TYR901 3.4 100.0 1.0 CG A:ASN899 3.5 95.5 1.0 CG A:ASP989 3.5 89.6 1.0 C A:ALA939 3.7 85.1 1.0 ND2 A:ASN899 3.9 89.7 1.0 CB A:ASP989 4.0 79.3 1.0 CB A:ASP933 4.0 75.5 1.0 N A:TYR901 4.1 0.0 1.0 CA A:TYR901 4.2 96.6 1.0 CB A:ASP931 4.3 83.9 1.0 OD1 A:ASP933 4.3 88.9 1.0 N A:PRO902 4.4 0.3 1.0 CA A:PRO902 4.5 89.7 1.0 OD1 A:ASP989 4.5 85.1 1.0 N A:SER940 4.6 82.1 1.0 CA A:ALA939 4.6 88.1 1.0 C A:PRO902 4.6 94.1 1.0 CA A:SER940 4.6 86.1 1.0 CB A:TYR901 4.7 95.1 1.0 CB A:ALA939 4.7 78.7 1.0 CD A:PRO903 4.8 78.0 1.0 CB A:ASN899 4.8 93.7 1.0 N A:ASP933 4.8 86.4 1.0 N A:PRO903 4.9 83.9 1.0 O A:PRO902 5.0 94.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human Protocadherin-15 EC8-10


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 EC8-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:91.8 occ:1.00 OD1 A:ASP897 2.3 79.2 1.0 OD1 A:ASP900 2.3 0.1 1.0 O A:MET898 2.3 0.1 1.0 OE2 A:GLU862 2.5 95.6 1.0 OE2 A:GLU809 2.6 95.7 1.0 OE1 A:GLU862 2.8 98.0 1.0 CD A:GLU862 3.0 95.9 1.0 CG A:ASP900 3.4 99.8 1.0 CG A:ASP897 3.5 87.4 1.0 C A:MET898 3.5 98.2 1.0 N A:MET898 3.7 87.1 1.0 CD A:GLU809 3.7 94.3 1.0 OD2 A:ASP897 4.0 89.6 1.0 OD2 A:ASP900 4.1 0.5 1.0 CA A:MET898 4.2 94.7 1.0 OE1 A:GLU809 4.2 94.5 1.0 CA A:CA2003 4.3 94.4 1.0 CB A:ASP900 4.4 97.8 1.0 N A:ASP900 4.4 90.6 1.0 OD1 A:ASP933 4.5 88.9 1.0 CG A:GLU862 4.5 87.7 1.0 N A:ASN899 4.6 87.4 1.0 C A:ASP897 4.6 91.2 1.0 CB A:ASP897 4.7 91.4 1.0 CB A:TYR861 4.7 82.3 1.0 CA A:ASP897 4.7 96.2 1.0 CA A:ASN899 4.8 93.4 1.0 C A:ASN899 4.8 87.7 1.0 CG A:GLU809 4.8 85.7 1.0 CA A:ASP900 5.0 95.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human Protocadherin-15 EC8-10


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 EC8-10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:94.4 occ:1.00 OD2 A:ASP900 2.3 0.5 1.0 OE1 A:GLU862 2.3 98.0 1.0 OD1 A:ASP860 2.4 97.1 1.0 O A:HOH2168 2.4 78.2 1.0 OE1 A:GLU809 2.8 94.5 1.0 CG A:ASP900 3.1 99.8 1.0 CG A:ASP860 3.3 82.8 1.0 OD1 A:ASP900 3.4 0.1 1.0 CD A:GLU862 3.5 95.9 1.0 CD A:GLU809 3.7 94.3 1.0 OD2 A:ASP860 3.8 81.6 1.0 OE2 A:GLU809 3.8 95.7 1.0 CB A:GLU862 3.9 88.6 1.0 N A:GLU862 4.1 83.5 1.0 CG A:GLU862 4.2 87.7 1.0 CA A:CA2002 4.3 91.8 1.0 CB A:ASP860 4.3 76.0 1.0 N A:TYR861 4.4 74.0 1.0 CB A:ASP900 4.4 97.8 1.0 CA A:ASP860 4.5 72.8 1.0 OE2 A:GLU862 4.5 95.6 1.0 C A:ASP860 4.6 74.6 1.0 CA A:GLU862 4.6 88.3 1.0 ND2 A:ASN810 4.8 83.7 1.0 OD1 A:ASN810 4.8 84.6 1.0

R.Araya-Secchi, B.L.Neel, M.Sotomayor. An Elastic Element in the Protocadherin-15 Tip Link of the Inner Ear. Nat Commun V. 7 13458 2016.
ISSN: ESSN 2041-1723
PubMed: 27857071
DOI: 10.1038/NCOMMS13458