Calcium in PDB 2whv: Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium)

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium), PDB code: 2whv was solved by M.Sotomayor, W.Weihofen, R.Gaudet, D.P.Corey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.25 / 2.36
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	151.290, 151.290, 136.881, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.1

The structure of Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium) also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium) (pdb code 2whv). 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 EC1-2 (All Cation Binding Sites Occupied By Calcium), PDB code: 2whv:
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 EC1-2 (All Cation Binding Sites Occupied By Calcium)


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 EC1-2 (All Cation Binding Sites Occupied By Calcium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:23.5 occ:1.00 O A:ARG5 2.2 27.6 1.0 OD2 A:ASP41 2.2 24.6 1.0 OD2 A:ASP87 2.4 12.1 1.0 OD1 A:ASP37 2.4 23.0 1.0 OD2 A:ASP39 2.5 23.6 1.0 OD1 A:ASN4 2.5 29.1 1.0 OD2 A:ASP37 2.7 22.0 1.0 CG A:ASP37 2.9 23.0 1.0 CG A:ASP41 3.4 25.3 1.0 C A:ARG5 3.4 28.8 1.0 CG A:ASP87 3.5 15.0 1.0 CG A:ASN4 3.5 32.2 1.0 CG A:ASP39 3.5 24.5 1.0 CB A:ASP87 3.8 16.0 1.0 ND2 A:ASN4 3.8 29.9 1.0 CB A:ASP39 3.9 24.9 1.0 N A:ARG5 3.9 30.2 1.0 CB A:ASP41 4.0 25.4 1.0 O A:HOH2004 4.1 33.4 1.0 CA A:ARG5 4.2 29.7 1.0 O A:HOH2116 4.2 47.0 1.0 N A:LEU6 4.3 28.1 1.0 OD1 A:ASP41 4.4 26.8 1.0 CB A:ASP37 4.4 21.5 1.0 CA A:LEU6 4.5 27.8 1.0 OD1 A:ASP87 4.6 12.2 1.0 OD1 A:ASP39 4.6 25.0 1.0 N A:ASP39 4.7 24.6 1.0 C A:LEU6 4.8 27.6 1.0 CB A:ARG5 4.8 29.6 1.0 C A:ASN4 4.8 31.9 1.0 CB A:ASN4 4.8 32.8 1.0 CD A:PRO7 4.8 27.8 1.0 CA A:ASP39 4.9 24.5 1.0 N A:PRO7 4.9 27.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium)


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 EC1-2 (All Cation Binding Sites Occupied By Calcium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:22.3 occ:1.00 OD2 A:ASP105 2.2 24.7 1.0 OE2 A:GLU22 2.3 22.3 1.0 OE2 A:GLU74 2.3 20.7 1.0 OD2 A:ASP72 2.3 22.7 1.0 O A:HOH2123 2.4 20.4 1.0 O A:HOH2126 2.4 18.1 1.0 CG A:ASP105 3.0 26.5 1.0 OD1 A:ASP105 3.0 25.5 1.0 CD A:GLU22 3.3 23.2 1.0 CG A:ASP72 3.3 24.2 1.0 CD A:GLU74 3.5 21.8 1.0 OE1 A:GLU22 3.8 23.1 1.0 CA A:CA403 4.0 23.7 1.0 OD1 A:ASP72 4.1 24.9 1.0 CA A:ASP72 4.1 23.2 1.0 CB A:ASP72 4.1 23.4 1.0 O A:HOH2095 4.2 24.7 1.0 ND2 A:ASN106 4.2 26.9 1.0 N A:ARG73 4.3 22.7 1.0 O A:HOH2124 4.3 30.8 1.0 OE1 A:GLU74 4.4 21.3 1.0 CB A:ASP105 4.4 26.2 1.0 CG A:GLU74 4.4 22.8 1.0 N A:GLU74 4.4 23.1 1.0 CB A:GLU74 4.4 23.2 1.0 O A:HOH2122 4.5 31.1 1.0 C A:ASP72 4.5 22.7 1.0 CG A:GLU22 4.5 24.7 1.0 O A:HOH2094 4.5 19.3 1.0 O A:HOH2036 4.6 32.9 1.0 O A:HOH2125 4.7 39.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium)


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 EC1-2 (All Cation Binding Sites Occupied By Calcium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.7 occ:1.00 OD1 A:ASP102 2.3 21.8 1.0 OD1 A:ASP138 2.3 23.7 1.0 OE1 A:GLU74 2.3 21.3 1.0 O A:VAL103 2.3 26.1 1.0 OD1 A:ASP105 2.4 25.5 1.0 OE1 A:GLU22 2.4 23.1 1.0 OE2 A:GLU74 2.7 20.7 1.0 CD A:GLU74 2.8 21.8 1.0 CG A:ASP102 3.3 24.9 1.0 CD A:GLU22 3.4 23.2 1.0 CG A:ASP138 3.4 23.9 1.0 CG A:ASP105 3.5 26.5 1.0 C A:VAL103 3.5 25.8 1.0 OE2 A:GLU22 3.7 22.3 1.0 OD2 A:ASP102 3.8 25.4 1.0 ND2 A:ASN106 3.8 26.9 1.0 N A:VAL103 3.9 25.4 1.0 CA A:CA402 4.0 22.3 1.0 N A:ASP105 4.0 26.2 1.0 OD2 A:ASP105 4.0 24.7 1.0 CB A:ASP138 4.1 23.7 1.0 CG A:GLU74 4.3 22.8 1.0 CA A:ASP138 4.3 24.1 1.0 CA A:VAL103 4.4 25.5 1.0 OD2 A:ASP138 4.4 23.4 1.0 NE A:ARG73 4.5 24.1 1.0 N A:ASN104 4.5 25.8 1.0 CB A:ASP102 4.5 24.8 1.0 CB A:ASP105 4.6 26.2 1.0 CA A:ASP102 4.6 24.9 1.0 CA A:ASN104 4.7 26.4 1.0 CG2 A:VAL103 4.7 26.2 1.0 C A:ASP102 4.8 24.9 1.0 CG A:GLU22 4.8 24.7 1.0 CA A:ASP105 4.8 26.2 1.0 NH1 A:ARG73 4.8 27.4 1.0 C A:ASN104 4.8 26.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Mouse Cadherin-23 EC1-2 (All Cation Binding Sites Occupied By Calcium)


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 EC1-2 (All Cation Binding Sites Occupied By Calcium) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:25.0 occ:1.00 O A:GLY142 2.3 24.0 1.0 OD1 A:ASN104 2.3 27.1 1.0 O A:ASN106 2.3 26.9 1.0 OD2 A:ASP187 2.4 23.1 1.0 OD2 A:ASP136 2.4 26.7 1.0 OD1 A:ASP136 2.5 29.5 1.0 OD2 A:ASP138 2.5 23.4 1.0 CG A:ASP136 2.8 27.9 1.0 CG A:ASP187 3.3 25.9 1.0 CG A:ASN104 3.4 26.5 1.0 C A:GLY142 3.4 24.0 1.0 CG A:ASP138 3.5 23.9 1.0 C A:ASN106 3.5 27.0 1.0 CB A:ASP138 3.7 23.7 1.0 CB A:ASP187 3.7 26.3 1.0 ND2 A:ASN104 4.0 24.0 1.0 CA A:GLY142 4.2 23.5 1.0 N A:ASN106 4.3 26.6 1.0 CA A:ASN106 4.3 26.9 1.0 CB A:ASP136 4.3 26.9 1.0 OD1 A:ASP187 4.4 24.1 1.0 CB A:ASN106 4.4 27.2 1.0 N A:GLY143 4.5 24.9 1.0 N A:ALA107 4.5 27.0 1.0 OD1 A:ASP138 4.6 23.7 1.0 CA A:GLY143 4.7 25.7 1.0 CB A:ASN104 4.7 26.0 1.0 CA A:ALA107 4.7 26.9 1.0 N A:ASP138 4.8 24.1 1.0 CA A:ASP138 4.8 24.1 1.0 CA A:ASN104 4.9 26.4 1.0 C A:ALA107 4.9 26.9 1.0 CB A:LEU194 5.0 32.4 1.0

M.Sotomayor, W.Weihofen, R.Gaudet, D.P.Corey. Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Neuron V. 66 85 2010.
ISSN: ISSN 0896-6273
PubMed: 20399731
DOI: 10.1016/J.NEURON.2010.03.028