Calcium in PDB 5tfl: Crystal Structure of Mouse Cadherin-23 EC7+8

The structure of Crystal Structure of Mouse Cadherin-23 EC7+8, PDB code: 5tfl was solved by A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	131.39 / 3.56
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	185.809, 185.809, 185.809, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.1

The structure of Crystal Structure of Mouse Cadherin-23 EC7+8 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC7+8 (pdb code 5tfl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-23 EC7+8, PDB code: 5tfl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC7+8


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 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:58.9 occ:1.00 OD1 A:ASP747 2.2 74.5 1.0 OE2 A:GLU659 2.3 78.7 1.0 OE1 A:GLU714 2.3 67.2 1.0 OD1 A:ASP783 2.3 71.0 1.0 O A:ILE748 2.5 85.2 1.0 OD1 A:ASP750 2.6 85.1 1.0 OE2 A:GLU714 2.8 69.2 1.0 CD A:GLU714 2.8 70.6 1.0 CD A:GLU659 3.2 75.1 1.0 CG A:ASP783 3.4 69.8 1.0 CG A:ASP747 3.5 77.4 1.0 CG A:ASP750 3.5 85.6 1.0 C A:ILE748 3.6 82.2 1.0 OE1 A:GLU659 3.7 75.1 1.0 N A:ILE748 3.7 78.7 1.0 OD2 A:ASP750 3.9 87.3 1.0 ND2 A:ASN751 4.0 75.6 1.0 OD2 A:ASP747 4.1 79.2 1.0 CB A:ASP783 4.1 69.3 1.0 CA A:ILE748 4.2 82.8 1.0 OD2 A:ASP783 4.2 71.3 1.0 CG A:GLU714 4.2 75.1 1.0 N A:ASP750 4.3 73.8 1.0 CG A:GLU659 4.3 72.4 1.0 NE A:ARG713 4.5 71.8 1.0 CA A:ASP783 4.5 69.7 1.0 CB A:ASP747 4.5 77.9 1.0 C A:ASP747 4.5 79.5 1.0 CA A:ASP747 4.6 77.7 1.0 NH1 A:ARG713 4.6 74.0 1.0 NA A:NA901 4.6 71.1 1.0 N A:ASN749 4.7 78.9 1.0 CB A:ASP750 4.8 82.5 1.0 CG2 A:ILE748 4.8 82.2 1.0 CA A:ASN749 4.9 77.8 1.0 CB A:ARG713 4.9 70.0 1.0 CA A:ASP750 5.0 75.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC7+8


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 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:62.4 occ:1.00 OD1 A:ASN749 2.2 75.4 1.0 OD2 A:ASP839 2.2 72.4 1.0 O A:ASN751 2.3 67.7 1.0 OD2 A:ASP783 2.6 71.3 1.0 O A:ASN787 2.6 65.2 1.0 OD1 A:ASP781 2.6 70.1 1.0 OD2 A:ASP781 2.6 67.1 1.0 CG A:ASP781 3.0 68.8 1.0 CG A:ASP839 3.4 70.7 1.0 CG A:ASN749 3.4 79.3 1.0 C A:ASN751 3.5 69.9 1.0 CG A:ASP783 3.6 69.8 1.0 C A:ASN787 3.7 68.2 1.0 CB A:ASP783 3.8 69.3 1.0 ND2 A:ASN749 4.0 83.0 1.0 N A:ASN751 4.0 72.0 1.0 CB A:ASP839 4.2 69.4 1.0 OD1 A:ASP839 4.2 70.8 1.0 CD1 A:LEU845 4.2 77.9 1.0 CA A:ASN751 4.2 71.2 1.0 CB A:ASP781 4.4 70.0 1.0 CB A:ASN751 4.4 70.9 1.0 CA A:ASN787 4.5 70.4 1.0 CB A:ASN787 4.5 70.8 1.0 N A:HIS752 4.6 69.7 1.0 CB A:ASN749 4.6 78.9 1.0 CA A:ASN749 4.6 77.8 1.0 N A:GLY788 4.7 72.1 1.0 OD1 A:ASP783 4.7 71.0 1.0 N A:ASP750 4.7 73.8 1.0 C A:ASN749 4.7 78.7 1.0 CA A:HIS752 4.8 69.3 1.0 CA A:GLY788 4.9 75.0 1.0 C A:HIS752 4.9 66.8 1.0 CB A:LEU845 5.0 71.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC7+8


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 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:81.1 occ:1.00 OD1 B:ASP747 2.0 80.7 1.0 OE1 B:GLU659 2.1 95.6 1.0 OD1 B:ASP783 2.2 89.0 1.0 OE1 B:GLU714 2.3 87.8 1.0 O B:ILE748 2.6 89.1 1.0 OD1 B:ASP750 2.8 95.3 1.0 CD B:GLU714 3.0 89.9 1.0 OE2 B:GLU714 3.1 90.9 1.0 CG B:ASP747 3.2 81.5 1.0 CG B:ASP783 3.2 86.6 1.0 CD B:GLU659 3.3 95.1 1.0 C B:ILE748 3.6 87.5 1.0 N B:ILE748 3.6 80.4 1.0 CG B:ASP750 3.8 97.4 1.0 OD2 B:ASP747 3.8 83.3 1.0 CB B:ASP783 3.9 83.6 1.0 OE2 B:GLU659 4.0 94.3 1.0 ND2 B:ASN751 4.1 90.8 1.0 OD2 B:ASP783 4.1 87.7 1.0 CA B:ILE748 4.2 84.3 1.0 OD2 B:ASP750 4.2 0.3 1.0 CA B:ASP783 4.2 82.4 1.0 NE B:ARG713 4.3 80.8 1.0 NH2 B:ARG713 4.3 85.4 1.0 CB B:ASP747 4.3 81.4 1.0 CG B:GLU714 4.3 90.5 1.0 N B:ASP750 4.4 90.6 1.0 CG B:GLU659 4.4 92.3 1.0 CA B:ASP747 4.4 81.9 1.0 C B:ASP747 4.4 79.8 1.0 N B:ASN749 4.6 89.3 1.0 CZ B:ARG713 4.8 82.5 1.0 NA B:NA901 4.8 95.8 1.0 CA B:ASN749 4.8 89.6 1.0 CB B:ASP750 4.9 97.8 1.0 CB B:ILE748 5.0 84.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC7+8


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 EC7+8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:72.2 occ:1.00 OD1 B:ASN749 2.2 92.5 1.0 OD2 B:ASP839 2.4 87.1 1.0 OD2 B:ASP783 2.4 87.7 1.0 O B:ASN787 2.5 81.5 1.0 OD1 B:ASP781 2.5 76.2 1.0 O B:ASN751 2.5 94.8 1.0 OD2 B:ASP781 2.7 78.9 1.0 CG B:ASP781 2.9 76.6 1.0 CG B:ASN749 3.4 94.4 1.0 CG B:ASP783 3.4 86.6 1.0 CG B:ASP839 3.5 85.8 1.0 C B:ASN787 3.6 81.3 1.0 CB B:ASP783 3.6 83.6 1.0 C B:ASN751 3.7 94.3 1.0 ND2 B:ASN749 4.0 96.5 1.0 N B:ASN751 4.1 93.1 1.0 CB B:ASP839 4.3 83.2 1.0 OD1 B:ASP839 4.3 89.5 1.0 CA B:ASN751 4.3 93.0 1.0 CB B:ASN787 4.3 82.0 1.0 CA B:ASN787 4.3 81.8 1.0 CB B:ASP781 4.4 76.5 1.0 CD1 B:LEU845 4.4 0.6 1.0 CB B:ASN751 4.5 90.3 1.0 CB B:ASN749 4.5 93.2 1.0 CA B:ASN749 4.6 89.6 1.0 N B:GLY788 4.6 80.8 1.0 OD1 B:ASP783 4.6 89.0 1.0 N B:ASP750 4.7 90.6 1.0 C B:ASN749 4.7 88.1 1.0 CA B:GLY788 4.7 82.7 1.0 N B:HIS752 4.8 97.4 1.0 CA B:ASP783 4.9 82.4 1.0 N B:ASP783 4.9 83.4 1.0 CA B:HIS752 5.0 97.0 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