Calcium in PDB 7skh: Crystal Structure of Mouse Cadherin-23 EC16-17

The structure of Crystal Structure of Mouse Cadherin-23 EC16-17, PDB code: 7skh was solved by J.C.Sudar, J.S.Sandhu, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.27 / 2.27
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.861, 90.861, 170.68, 90, 90, 90
R / Rfree (%)	20.9 / 25.2

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC16-17 (pdb code 7skh). 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 EC16-17, PDB code: 7skh:
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 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1901 b:41.7 occ:1.00 OE1 A:GLU1678 2.2 37.5 1.0 OD1 A:ASP1676 2.2 39.2 1.0 OE2 A:GLU1622 2.3 36.7 1.0 OD2 A:ASP1716 2.3 37.2 1.0 O A:HOH2046 2.4 34.9 1.0 O A:HOH2023 2.6 45.7 1.0 CG A:ASP1716 3.1 37.5 1.0 CD A:GLU1622 3.2 39.0 1.0 OD1 A:ASP1716 3.2 34.2 1.0 CG A:ASP1676 3.4 37.6 1.0 CD A:GLU1678 3.4 38.8 1.0 OE1 A:GLU1622 3.6 39.7 1.0 CA A:CA1902 3.9 37.5 1.0 OD2 A:ASP1676 4.2 37.9 1.0 N A:TYR1677 4.2 35.7 1.0 O A:HOH2013 4.2 39.4 1.0 CA A:ASP1676 4.2 36.3 1.0 ND2 A:ASN1717 4.2 36.7 1.0 CB A:ASP1676 4.3 36.7 1.0 OE2 A:GLU1678 4.3 41.7 1.0 CG A:GLU1678 4.3 40.0 1.0 N A:GLU1678 4.3 35.2 1.0 CG A:GLU1622 4.4 39.4 1.0 CB A:GLU1678 4.4 38.8 1.0 CB A:ASP1716 4.5 37.9 1.0 C A:ASP1676 4.6 35.9 1.0 CB A:GLU1622 5.0 39.3 1.0 OE2 A:GLU1674 5.0 55.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1902 b:37.5 occ:1.00 OD1 A:ASP1713 2.3 36.0 1.0 OD1 A:ASP1716 2.3 34.2 1.0 OE1 A:GLU1622 2.4 39.7 1.0 OE2 A:GLU1678 2.4 41.7 1.0 O A:ILE1714 2.4 35.7 1.0 OD1 A:ASP1749 2.5 36.7 1.0 OE1 A:GLU1678 2.7 37.5 1.0 CD A:GLU1678 2.9 38.8 1.0 CD A:GLU1622 3.4 39.0 1.0 CG A:ASP1716 3.4 37.5 1.0 CG A:ASP1713 3.5 38.9 1.0 CG A:ASP1749 3.5 37.5 1.0 C A:ILE1714 3.6 40.4 1.0 N A:ILE1714 3.8 39.8 1.0 OE2 A:GLU1622 3.9 36.7 1.0 CA A:CA1901 3.9 41.7 1.0 ND2 A:ASN1717 3.9 36.7 1.0 OD2 A:ASP1716 4.0 37.2 1.0 N A:ASP1716 4.1 36.8 1.0 CB A:ASP1749 4.2 37.2 1.0 OD2 A:ASP1713 4.2 39.6 1.0 CG A:GLU1678 4.3 40.0 1.0 CA A:ILE1714 4.3 41.2 1.0 OD2 A:ASP1749 4.5 36.7 1.0 CA A:ASP1749 4.5 37.0 1.0 CB A:TYR1677 4.5 38.4 1.0 CA A:ASP1713 4.5 38.5 1.0 C A:ASP1713 4.5 39.9 1.0 CB A:ASP1713 4.6 38.6 1.0 CB A:ASP1716 4.6 37.9 1.0 N A:ASN1715 4.7 39.4 1.0 CG A:GLU1622 4.7 39.4 1.0 CG1 A:ILE1714 4.8 47.1 1.0 CA A:ASP1716 4.8 38.1 1.0 CA A:ASN1715 4.9 38.3 1.0 O A:HOH2046 5.0 34.9 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1903 b:35.5 occ:1.00 O A:ASN1717 2.3 35.4 1.0 OD1 A:ASN1715 2.3 35.2 1.0 OD2 A:ASP1749 2.3 36.7 1.0 OD2 A:ASP1802 2.4 34.5 1.0 O A:ASN1753 2.4 33.3 1.0 OD2 A:ASP1747 2.4 33.2 1.0 OD1 A:ASP1747 2.6 37.0 1.0 CG A:ASP1747 2.8 34.6 1.0 CG A:ASP1802 3.4 35.1 1.0 CG A:ASP1749 3.4 37.5 1.0 CG A:ASN1715 3.5 36.8 1.0 C A:ASN1717 3.5 36.9 1.0 C A:ASN1753 3.6 34.6 1.0 CB A:ASP1802 3.8 34.4 1.0 CB A:ASP1749 3.8 37.2 1.0 ND2 A:ASN1715 4.1 36.1 1.0 N A:ASN1717 4.3 37.2 1.0 CA A:ASN1717 4.3 36.0 1.0 CB A:ASP1747 4.3 35.4 1.0 CA A:ASN1753 4.4 35.5 1.0 OD1 A:ASP1802 4.4 35.0 1.0 N A:GLY1754 4.5 37.7 1.0 OD1 A:ASP1749 4.5 36.7 1.0 CB A:ASN1717 4.5 34.0 1.0 N A:VAL1718 4.6 37.3 1.0 CD A:PRO1719 4.6 35.7 1.0 CA A:GLY1754 4.6 36.7 1.0 CB A:ASN1753 4.6 36.3 1.0 CD1 A:LEU1808 4.7 41.6 1.0 CB A:ASN1715 4.7 37.4 1.0 CA A:ASN1715 4.8 38.3 1.0 N A:PRO1719 4.9 35.1 1.0 CA A:VAL1718 4.9 36.9 1.0 N A:ASP1749 4.9 36.4 1.0 C A:VAL1718 5.0 35.4 1.0 CA A:ASP1749 5.0 37.0 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1901 b:59.7 occ:1.00 O B:ASN1717 2.3 53.5 1.0 O B:ASN1753 2.3 57.5 1.0 OD1 B:ASN1715 2.4 61.6 1.0 OD2 B:ASP1747 2.4 51.2 1.0 OD2 B:ASP1749 2.4 56.0 1.0 OD2 B:ASP1802 2.4 53.8 1.0 OD1 B:ASP1747 2.6 52.9 1.0 CG B:ASP1747 2.8 50.6 1.0 CG B:ASP1802 3.4 54.8 1.0 CG B:ASP1749 3.4 59.3 1.0 CG B:ASN1715 3.5 63.0 1.0 C B:ASN1717 3.5 51.0 1.0 C B:ASN1753 3.5 58.5 1.0 CB B:ASP1749 3.8 60.1 1.0 CB B:ASP1802 3.8 54.9 1.0 ND2 B:ASN1715 4.0 62.1 1.0 CA B:ASN1717 4.3 53.0 1.0 N B:ASN1717 4.3 54.8 1.0 CB B:ASP1747 4.3 49.5 1.0 CA B:ASN1753 4.4 61.8 1.0 CB B:ASN1717 4.5 52.0 1.0 CB B:ASN1753 4.5 62.7 1.0 OD1 B:ASP1802 4.5 55.7 1.0 N B:GLY1754 4.5 59.7 1.0 CD B:PRO1719 4.6 46.7 1.0 OD1 B:ASP1749 4.6 61.2 1.0 N B:VAL1718 4.6 50.6 1.0 CD1 B:LEU1808 4.6 59.0 1.0 CA B:GLY1754 4.6 58.1 1.0 N B:ASP1749 4.7 58.7 1.0 CB B:ASN1715 4.7 65.0 1.0 CA B:ASN1715 4.8 64.7 1.0 CA B:ASP1749 4.9 61.3 1.0 N B:PRO1719 4.9 44.9 1.0 CA B:VAL1718 4.9 48.3 1.0 C B:VAL1718 5.0 46.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1902 b:68.8 occ:1.00 OD1 B:ASP1749 2.3 61.2 1.0 OD1 B:ASP1713 2.3 61.6 1.0 OE1 B:GLU1678 2.5 61.9 1.0 OE2 B:GLU1622 2.5 62.8 1.0 OD1 B:ASP1716 2.6 66.9 1.0 O B:ILE1714 2.6 60.1 1.0 OE2 B:GLU1678 2.8 61.6 1.0 CD B:GLU1678 2.9 59.1 1.0 CG B:ASP1749 3.4 59.3 1.0 CD B:GLU1622 3.5 63.3 1.0 CG B:ASP1713 3.5 64.0 1.0 CG B:ASP1716 3.6 66.0 1.0 OE1 B:GLU1622 3.8 60.7 1.0 C B:ILE1714 3.8 68.8 1.0 ND2 B:ASN1717 3.8 53.4 1.0 N B:ILE1714 4.0 70.3 1.0 CA B:CA1903 4.0 62.7 1.0 CB B:ASP1749 4.1 60.1 1.0 OD2 B:ASP1716 4.2 67.6 1.0 N B:ASP1716 4.2 61.9 1.0 OD2 B:ASP1749 4.3 56.0 1.0 OD2 B:ASP1713 4.3 64.4 1.0 CA B:ASP1749 4.4 61.3 1.0 CG B:GLU1678 4.4 56.0 1.0 CA B:ILE1714 4.5 73.5 1.0 CA B:ASP1713 4.6 67.9 1.0 CB B:ASP1713 4.6 67.0 1.0 CB B:TYR1677 4.7 62.1 1.0 C B:ASP1713 4.7 70.8 1.0 O B:HOH2005 4.7 45.0 1.0 CB B:ASP1716 4.7 63.5 1.0 CG B:GLU1622 4.8 67.1 1.0 O B:HOH2035 4.8 52.9 1.0 N B:ASN1715 4.8 68.6 1.0 CG1 B:ILE1714 4.8 76.8 1.0 CA B:ASP1716 4.9 61.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Mouse Cadherin-23 EC16-17


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 EC16-17 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1903 b:62.7 occ:1.00 OD2 B:ASP1716 2.3 67.6 1.0 OE1 B:GLU1622 2.4 60.7 1.0 O B:HOH2035 2.4 52.9 1.0 OE2 B:GLU1678 2.4 61.6 1.0 OD1 B:ASP1676 2.4 57.3 1.0 O B:HOH2025 2.6 58.7 1.0 CG B:ASP1716 3.1 66.0 1.0 OD1 B:ASP1716 3.1 66.9 1.0 CD B:GLU1622 3.3 63.3 1.0 CG B:ASP1676 3.5 57.3 1.0 CD B:GLU1678 3.6 59.1 1.0 OE2 B:GLU1622 3.8 62.8 1.0 CA B:CA1902 4.0 68.8 1.0 CA B:ASP1676 4.2 59.4 1.0 N B:TYR1677 4.2 60.1 1.0 CB B:ASP1676 4.3 57.8 1.0 ND2 B:ASN1717 4.4 53.4 1.0 OD2 B:ASP1676 4.4 56.5 1.0 CG B:GLU1622 4.4 67.1 1.0 OE1 B:GLU1678 4.5 61.9 1.0 CG B:GLU1678 4.5 56.0 1.0 N B:GLU1678 4.6 53.9 1.0 C B:ASP1676 4.6 57.9 1.0 CB B:GLU1678 4.6 54.3 1.0 CB B:ASP1716 4.6 63.5 1.0 OE2 B:GLU1674 4.9 71.5 1.0

J.C.Sudar, J.S.Sandhu, M.Sotomayor. Crystal Structure of Mouse Cadherin-23 EC16-17 To Be Published.