Calcium in PDB 5tfm: Crystal Structure of Human Cadherin-23 EC6-8

The structure of Crystal Structure of Human Cadherin-23 EC6-8, PDB code: 5tfm 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)	80.89 / 2.92
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	93.407, 93.407, 122.386, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.6

The structure of Crystal Structure of Human Cadherin-23 EC6-8 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Cadherin-23 EC6-8 (pdb code 5tfm). 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 Cadherin-23 EC6-8, PDB code: 5tfm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Human Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:60.0 occ:1.00 O A:TYR681 2.2 59.2 1.0 OD1 A:ASN642 2.3 67.1 1.0 OD2 A:ASP676 2.4 57.1 1.0 O A:ASN644 2.4 57.4 1.0 OD2 A:ASP674 2.4 62.1 1.0 OD2 A:ASP727 2.5 65.6 1.0 OD1 A:ASP674 2.6 62.6 1.0 CG A:ASP674 2.8 61.3 1.0 CG A:ASN642 3.4 68.7 1.0 CG A:ASP727 3.4 66.7 1.0 C A:TYR681 3.4 62.0 1.0 CG A:ASP676 3.5 58.3 1.0 C A:ASN644 3.6 57.0 1.0 CB A:ASP727 3.6 66.1 1.0 CB A:ASP676 3.9 60.1 1.0 ND2 A:ASN642 4.0 70.3 1.0 N A:ASN644 4.3 57.7 1.0 CA A:ASN644 4.3 57.6 1.0 CA A:TYR681 4.3 64.2 1.0 CB A:TYR681 4.3 63.7 1.0 CB A:ASP674 4.3 62.0 1.0 N A:GLY682 4.3 64.4 1.0 CA A:GLY682 4.4 64.9 1.0 CB A:ASN644 4.4 58.4 1.0 OD1 A:ASP727 4.5 69.1 1.0 OD1 A:ASP676 4.5 58.5 1.0 N A:PRO645 4.6 56.8 1.0 CB A:ASN642 4.7 69.3 1.0 N A:ASP676 4.7 60.5 1.0 CA A:PRO645 4.8 57.1 1.0 CA A:ASN642 4.8 67.4 1.0 CA A:ASP676 4.9 60.7 1.0 CD A:PRO646 4.9 60.0 1.0 C A:ASN642 5.0 67.5 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Human Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:61.6 occ:1.00 OD1 A:ASP640 2.1 64.3 1.0 OE2 A:GLU607 2.2 59.1 1.0 OD1 A:ASP676 2.3 58.5 1.0 O A:GLU641 2.3 64.5 1.0 OE2 A:GLU549 2.4 62.2 1.0 OD1 A:ASP643 2.4 58.4 1.0 OE1 A:GLU607 2.7 58.4 1.0 CD A:GLU607 2.8 58.9 1.0 CG A:ASP640 3.2 66.8 1.0 CG A:ASP676 3.3 58.3 1.0 CD A:GLU549 3.4 62.5 1.0 CG A:ASP643 3.4 58.7 1.0 C A:GLU641 3.5 67.6 1.0 OD2 A:ASP640 3.6 68.1 1.0 OE1 A:GLU549 3.7 62.9 1.0 N A:GLU641 3.7 68.8 1.0 N A:ASP643 3.9 58.8 1.0 CB A:ASP676 3.9 60.1 1.0 CA A:CA903 4.0 65.3 1.0 OD2 A:ASP643 4.0 60.8 1.0 ND2 A:ASN644 4.1 58.2 1.0 CG A:GLU607 4.2 60.0 1.0 CA A:GLU641 4.2 70.3 1.0 OD2 A:ASP676 4.3 57.1 1.0 CA A:ASP676 4.4 60.7 1.0 CB A:TYR606 4.4 58.7 1.0 N A:ASN642 4.5 68.2 1.0 CB A:ASP640 4.5 68.5 1.0 CB A:ASP643 4.5 59.0 1.0 CA A:ASN642 4.6 67.4 1.0 C A:ASP640 4.6 68.5 1.0 CA A:ASP643 4.6 58.7 1.0 CG A:GLU549 4.6 63.8 1.0 CA A:ASP640 4.6 66.8 1.0 O A:HOH1006 4.6 48.7 1.0 CB A:GLU641 4.7 73.6 1.0 C A:ASN642 4.8 67.5 1.0 CD2 A:TYR606 4.9 60.0 1.0 N A:ARG677 4.9 64.8 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Human Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:65.3 occ:1.00 OD1 A:ASP605 2.0 66.3 1.0 O A:HOH1006 2.2 48.7 1.0 OE1 A:GLU549 2.3 62.9 1.0 OE1 A:GLU607 2.3 58.4 1.0 OD2 A:ASP643 2.4 60.8 1.0 CG A:ASP643 3.1 58.7 1.0 OD1 A:ASP643 3.2 58.4 1.0 CD A:GLU549 3.2 62.5 1.0 CG A:ASP605 3.2 64.4 1.0 OE2 A:GLU549 3.4 62.2 1.0 CD A:GLU607 3.6 58.9 1.0 OD1 A:ASN550 3.9 65.3 1.0 OD2 A:ASP605 4.0 67.1 1.0 CA A:CA902 4.0 61.6 1.0 ND2 A:ASN550 4.0 62.5 1.0 N A:TYR606 4.1 57.7 1.0 CA A:ASP605 4.1 60.8 1.0 CB A:ASP605 4.2 62.1 1.0 O A:HOH1007 4.3 60.8 1.0 N A:GLU607 4.4 59.8 1.0 OE2 A:GLU607 4.4 59.1 1.0 CG A:ASN550 4.4 64.4 1.0 C A:ASP605 4.4 58.9 1.0 CG A:GLU607 4.5 60.0 1.0 CB A:GLU607 4.5 60.7 1.0 CG A:GLU549 4.5 63.8 1.0 ND2 A:ASN644 4.6 58.2 1.0 CB A:ASP643 4.6 59.0 1.0 CB A:GLU549 4.9 62.3 1.0 CA A:TYR606 5.0 57.5 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Human Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:87.8 occ:1.00 OD1 A:ASP747 2.2 81.4 1.0 OD1 A:ASP750 2.2 91.8 1.0 OE1 A:GLU659 2.2 83.3 1.0 OD1 A:ASP783 2.3 90.4 1.0 OE1 A:GLU714 2.4 84.5 1.0 O A:ILE748 2.5 92.1 1.0 OE2 A:GLU714 2.7 94.1 1.0 CD A:GLU714 2.8 89.5 1.0 CD A:GLU659 3.2 85.4 1.0 CG A:ASP783 3.3 87.9 1.0 CG A:ASP747 3.3 82.1 1.0 CG A:ASP750 3.4 94.3 1.0 OE2 A:GLU659 3.5 83.8 1.0 C A:ILE748 3.7 95.0 1.0 N A:ILE748 3.8 89.5 1.0 OD2 A:ASP747 3.9 82.6 1.0 CB A:ASP783 4.0 85.0 1.0 OD2 A:ASP783 4.1 90.2 1.0 OD2 A:ASP750 4.1 95.4 1.0 N A:ASP750 4.2 91.5 1.0 CA A:ASP783 4.2 84.1 1.0 CG A:GLU714 4.3 90.3 1.0 CA A:ILE748 4.3 94.3 1.0 ND2 A:ASN751 4.4 97.0 1.0 NE A:ARG713 4.4 81.5 1.0 NA A:NA904 4.5 97.1 1.0 CB A:ASP747 4.5 81.4 1.0 CB A:ASP750 4.5 95.7 1.0 CG A:GLU659 4.5 88.3 1.0 CA A:ASP747 4.5 82.6 1.0 C A:ASP747 4.6 86.5 1.0 N A:ASN749 4.7 98.4 1.0 CA A:ASP750 4.8 92.7 1.0 CB A:ILE748 4.8 97.7 1.0 CB A:ARG713 4.9 84.2 1.0 CA A:ASN749 4.9 99.1 1.0 N A:ASP783 5.0 82.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Human Cadherin-23 EC6-8


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 Cadherin-23 EC6-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:86.8 occ:1.00 OD1 A:ASN749 2.3 98.7 1.0 O A:ASN751 2.4 92.7 1.0 O A:ASN787 2.4 81.5 1.0 OD2 A:ASP781 2.5 87.3 1.0 OD2 A:ASP783 2.6 90.2 1.0 OD1 A:ASP781 2.6 89.8 1.0 CG A:ASP781 2.9 86.4 1.0 OD2 A:ASP839 2.9 87.0 1.0 CG A:ASP783 3.5 87.9 1.0 CG A:ASN749 3.5 0.4 1.0 C A:ASN787 3.5 85.6 1.0 C A:ASN751 3.6 95.2 1.0 CG A:ASP839 3.6 86.1 1.0 CB A:ASP783 3.8 85.0 1.0 CB A:ASP839 4.1 83.7 1.0 N A:ASN751 4.2 94.1 1.0 CA A:ASN751 4.2 95.6 1.0 ND2 A:ASN749 4.3 0.1 1.0 CA A:ASN787 4.3 89.7 1.0 CB A:ASN787 4.3 91.8 1.0 CB A:ASN751 4.3 94.5 1.0 CB A:ASP781 4.4 84.3 1.0 OD1 A:ASP839 4.5 88.0 1.0 N A:GLY788 4.5 86.6 1.0 CA A:ASN749 4.6 99.1 1.0 CB A:ASN749 4.6 0.3 1.0 N A:HIS752 4.6 98.3 1.0 OD1 A:ASP783 4.6 90.4 1.0 C A:ASN749 4.8 0.5 1.0 CD1 A:LEU845 4.8 0.0 1.0 CA A:GLY788 4.8 86.7 1.0 N A:ASP750 4.9 91.5 1.0 CA A:HIS752 4.9 98.3 1.0 CD A:PRO753 4.9 89.0 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