Calcium in PDB 5wjm: Crystal Structure of Mouse Cadherin-23 EC17-18

The structure of Crystal Structure of Mouse Cadherin-23 EC17-18, PDB code: 5wjm was solved by 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)	86.60 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.476, 122.476, 43.603, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 26.6

The structure of Crystal Structure of Mouse Cadherin-23 EC17-18 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC17-18 (pdb code 5wjm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC17-18, PDB code: 5wjm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2001 b:34.9 occ:1.00 O A:ASN1753 2.1 31.9 1.0 O A:ASN1717 2.3 33.1 1.0 OD2 A:ASP1802 2.3 26.7 1.0 OD2 A:ASP1747 2.4 37.1 1.0 OD1 A:ASP1716 2.5 37.2 1.0 OD2 A:ASP1749 2.5 37.9 1.0 OD1 A:ASP1747 2.9 38.8 1.0 CG A:ASP1747 3.0 39.6 1.0 CG A:ASP1802 3.3 28.4 1.0 C A:ASN1753 3.4 31.9 1.0 C A:ASN1717 3.5 33.5 1.0 CG A:ASP1749 3.6 39.9 1.0 CG A:ASP1716 3.7 36.9 1.0 CB A:ASP1802 3.7 28.4 1.0 N A:ASN1717 3.9 36.2 1.0 CB A:ASP1749 4.1 41.4 1.0 OD2 A:ASP1716 4.2 36.5 1.0 CA A:ASN1717 4.2 35.5 1.0 CA A:ASN1753 4.2 31.8 1.0 N A:GLY1754 4.3 32.6 1.0 CD A:PRO1719 4.3 27.6 1.0 CB A:ASN1753 4.3 33.2 1.0 OD1 A:ASP1802 4.4 29.0 1.0 CA A:GLY1754 4.4 31.9 1.0 CB A:ASP1747 4.5 42.1 1.0 N A:VAL1718 4.5 32.1 1.0 N A:PRO1719 4.6 28.8 1.0 OD1 A:ASP1749 4.7 38.7 1.0 CB A:ASN1717 4.7 35.6 1.0 C A:ASP1716 4.7 35.3 1.0 C A:VAL1718 4.7 30.9 1.0 CA A:VAL1718 4.8 31.0 1.0 CB A:ASP1716 4.9 36.0 1.0 CA A:ASP1716 4.9 36.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:30.2 occ:1.00 OD2 A:ASP1823 2.1 25.1 1.0 OD1 A:ASP1787 2.1 26.9 1.0 OE1 A:GLU1733 2.3 23.8 1.0 OE2 A:GLU1789 2.3 19.6 1.0 CG A:ASP1823 3.2 24.1 1.0 CG A:ASP1787 3.2 26.9 1.0 CD A:GLU1733 3.4 24.9 1.0 OD1 A:ASP1823 3.6 24.3 1.0 CD A:GLU1789 3.6 20.0 1.0 OE2 A:GLU1733 3.8 25.1 1.0 CB A:ASP1787 4.1 24.8 1.0 O A:HOH2107 4.1 11.5 1.0 OD2 A:ASP1787 4.1 28.6 1.0 CA A:ASP1787 4.2 23.4 1.0 OE1 A:GLU1789 4.4 19.1 1.0 N A:ARG1788 4.4 21.8 1.0 CB A:ASP1823 4.5 23.4 1.0 CA A:CA2003 4.5 21.3 1.0 CG A:GLU1789 4.6 20.6 1.0 CB A:GLU1789 4.6 20.9 1.0 N A:GLU1789 4.6 21.9 1.0 CG A:GLU1733 4.6 25.6 1.0 C A:ASP1787 4.6 22.0 1.0 ND2 A:ASN1824 4.6 23.8 1.0 CB A:GLU1733 5.0 26.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:21.3 occ:1.00 OD1 A:ASP1820 2.2 18.9 1.0 OD1 A:ASP1823 2.2 24.3 1.0 OE2 A:GLU1733 2.3 25.1 1.0 OE1 A:GLU1789 2.3 19.1 1.0 OD1 A:ASP1856 2.3 19.4 1.0 O A:ILE1821 2.5 21.6 1.0 CD A:GLU1789 3.1 20.0 1.0 OE2 A:GLU1789 3.2 19.6 1.0 CG A:ASP1820 3.3 19.6 1.0 CG A:ASP1856 3.4 20.1 1.0 CD A:GLU1733 3.4 24.9 1.0 CG A:ASP1823 3.4 24.1 1.0 C A:ILE1821 3.7 21.9 1.0 ND2 A:ASN1824 3.7 23.8 1.0 N A:ILE1821 3.8 20.6 1.0 OD2 A:ASP1820 3.8 20.1 1.0 OE1 A:GLU1733 3.9 23.8 1.0 CB A:ASP1856 4.0 19.9 1.0 OD2 A:ASP1823 4.0 25.1 1.0 CA A:ASP1856 4.2 19.4 1.0 NE A:ARG1788 4.2 26.1 1.0 N A:ASP1823 4.2 22.4 1.0 OD2 A:ASP1856 4.4 19.9 1.0 CA A:ILE1821 4.4 21.4 1.0 CB A:ASP1820 4.4 19.8 1.0 NH2 A:ARG1788 4.5 27.9 1.0 CA A:ASP1820 4.5 19.9 1.0 CG A:GLU1789 4.5 20.6 1.0 CA A:CA2002 4.5 30.2 1.0 C A:ASP1820 4.6 20.0 1.0 CB A:ASP1823 4.6 23.4 1.0 CG A:GLU1733 4.7 25.6 1.0 N A:ASN1822 4.7 22.0 1.0 CG1 A:ILE1821 4.8 21.4 1.0 CA A:ASN1822 4.9 22.5 1.0 CZ A:ARG1788 4.9 26.4 1.0 CA A:ASP1823 4.9 22.6 1.0 CB A:ARG1788 4.9 22.2 1.0 N A:ASP1856 5.0 19.9 1.0 CG A:ASN1824 5.0 22.3 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:18.2 occ:1.00 OD2 A:ASP1856 2.2 19.9 1.0 OD1 A:ASN1822 2.3 22.5 1.0 OD1 A:ASP1854 2.4 20.0 1.0 OD2 A:ASP1907 2.4 26.4 1.0 O A:ASN1860 2.4 19.4 1.0 O A:ASN1824 2.5 21.1 1.0 OD2 A:ASP1854 2.6 19.2 1.0 CG A:ASP1854 2.8 20.2 1.0 CG A:ASP1856 3.3 20.1 1.0 CG A:ASP1907 3.5 26.4 1.0 CG A:ASN1822 3.5 23.2 1.0 C A:ASN1824 3.6 21.9 1.0 C A:ASN1860 3.6 19.8 1.0 CB A:ASP1856 3.7 19.9 1.0 CB A:ASP1907 4.0 25.5 1.0 ND2 A:ASN1822 4.2 23.9 1.0 N A:ASN1824 4.3 22.0 1.0 CA A:ASN1824 4.4 21.7 1.0 CB A:ASP1854 4.4 20.1 1.0 OD1 A:ASP1856 4.4 19.4 1.0 CB A:ASN1824 4.4 21.9 1.0 CB A:ASN1860 4.4 19.2 1.0 OD1 A:ASP1907 4.5 28.3 1.0 CA A:ASN1860 4.5 19.8 1.0 CD A:ARG1916 4.6 30.8 1.0 N A:ALA1861 4.6 20.3 1.0 CB A:ASN1822 4.7 22.9 1.0 CA A:ALA1861 4.7 20.9 1.0 N A:ASP1825 4.7 22.7 1.0 N A:ASP1856 4.8 19.9 1.0 C A:ASP1825 4.8 21.5 1.0 CA A:ASN1822 4.8 22.5 1.0 CD A:PRO1826 4.8 19.5 1.0 N A:PRO1826 4.9 19.8 1.0 CA A:ASP1856 4.9 19.4 1.0 CA A:ASP1825 5.0 23.4 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:34.8 occ:1.00 OE1 A:GLU1894 2.3 40.6 1.0 OD1 A:ASP1928 2.4 45.6 1.0 O A:GLU1929 2.4 51.6 1.0 OD1 A:ASP1931 2.4 65.9 1.0 OE2 A:GLU1839 2.6 37.2 1.0 CD A:GLU1894 3.2 41.9 1.0 CG A:ASP1931 3.3 67.1 1.0 CG A:ASP1928 3.3 46.1 1.0 OD2 A:ASP1931 3.4 68.8 1.0 OE2 A:GLU1894 3.4 42.1 1.0 C A:GLU1929 3.5 53.8 1.0 OD2 A:ASP1928 3.6 49.0 1.0 CD A:GLU1839 3.6 35.8 1.0 N A:GLU1929 3.8 49.3 1.0 O A:ASN1930 3.8 59.6 1.0 OE1 A:GLU1839 4.0 36.9 1.0 CA A:CA2006 4.0 49.2 1.0 C A:ASN1930 4.2 64.2 1.0 CA A:GLU1929 4.3 51.6 1.0 CG A:GLU1894 4.5 41.2 1.0 N A:ASN1930 4.5 58.7 1.0 CB A:ASP1928 4.6 43.2 1.0 CA A:ASN1930 4.6 63.5 1.0 NH2 A:ARG1893 4.7 65.4 1.0 CB A:ASP1931 4.7 64.7 1.0 CA A:ASP1928 4.7 40.9 1.0 C A:ASP1928 4.8 43.9 1.0 NE A:ARG1893 4.8 59.0 1.0 N A:ASP1931 4.9 65.1 1.0 CG A:GLU1839 4.9 33.6 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC17-18


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 Mouse Cadherin-23 EC17-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:49.2 occ:1.00 OD1 A:ASP1892 2.3 37.4 1.0 OD2 A:ASP1931 2.4 68.8 1.0 OE1 A:GLU1839 2.5 36.9 1.0 OE2 A:GLU1894 3.0 42.1 1.0 CD A:GLU1839 3.1 35.8 1.0 OE2 A:GLU1839 3.2 37.2 1.0 CG A:ASP1931 3.5 67.1 1.0 CG A:ASP1892 3.5 38.1 1.0 O A:ASN1930 3.7 59.6 1.0 CA A:CA2005 4.0 34.8 1.0 CD A:GLU1894 4.1 41.9 1.0 OD1 A:ASP1931 4.1 65.9 1.0 CG A:GLU1839 4.3 33.6 1.0 OD2 A:ASP1892 4.3 37.8 1.0 OD1 A:ASN1840 4.4 28.8 1.0 OE1 A:GLU1894 4.5 40.6 1.0 CB A:ASP1931 4.5 64.7 1.0 CB A:ASP1892 4.6 36.7 1.0 CA A:ASP1892 4.6 35.3 1.0 N A:ARG1893 4.7 36.0 1.0 C A:ASN1930 4.8 64.2 1.0 CA A:ASP1931 4.8 62.1 1.0

A.Jaiganesh, P.De-La-Torre, A.A.Patel, D.J.Termine, F.Velez-Cortes, C.Chen, M.Sotomayor. Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Structure V. 26 1210 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003