Calcium in PDB 3mvs: Structure of the N-Terminus of Cadherin 23

The structure of Structure of the N-Terminus of Cadherin 23, PDB code: 3mvs was solved by P.Clark, J.S.Joseph, A.R.Kolatkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.00 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.375, 64.208, 47.859, 90.00, 110.89, 90.00
R / Rfree (%)	16.3 / 18.8

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

Calcium binding site 1 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca211 b:12.4 occ:1.00 O A:HOH335 2.3 18.3 1.0 OE1 A:GLU73 2.3 13.8 1.0 OE1 A:GLU21 2.3 11.4 1.0 OD1 A:ASP71 2.3 14.9 1.0 O A:HOH395 2.4 15.3 1.0 OD2 A:ASP104 2.4 12.7 1.0 OD1 A:ASP104 3.1 10.7 1.0 CG A:ASP104 3.1 11.2 1.0 CD A:GLU21 3.2 10.7 1.0 CG A:ASP71 3.4 14.7 1.0 CD A:GLU73 3.6 12.9 1.0 OE2 A:GLU21 3.6 10.5 1.0 CA A:CA212 4.0 10.8 1.0 CA A:ASP71 4.1 13.4 1.0 N A:ARG72 4.1 11.8 1.0 OD2 A:ASP71 4.2 17.5 1.0 CB A:ASP71 4.2 14.1 1.0 O A:HOH401 4.2 19.2 1.0 ND2 A:ASN105 4.3 12.2 1.0 N A:GLU73 4.4 12.7 1.0 CG A:GLU21 4.4 10.3 1.0 OE2 A:GLU73 4.4 14.7 1.0 O A:HOH462 4.4 24.6 1.0 CB A:GLU73 4.5 14.3 1.0 CG A:GLU73 4.5 14.2 1.0 C A:ASP71 4.5 12.5 1.0 O A:HOH371 4.5 21.1 1.0 O A:HOH323 4.5 18.8 1.0 CB A:ASP104 4.6 11.1 1.0 O A:HOH507 4.7 35.9 1.0 O A:HOH474 4.9 39.6 1.0 CB A:GLU21 4.9 10.1 1.0

Calcium binding site 2 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca212 b:10.8 occ:1.00 OD1 A:ASP101 2.3 12.6 1.0 OD1 A:ASP137 2.3 10.9 1.0 OE2 A:GLU21 2.3 10.5 1.0 O A:VAL102 2.4 10.6 1.0 OE2 A:GLU73 2.4 14.7 1.0 OD1 A:ASP104 2.4 10.7 1.0 OE1 A:GLU73 2.7 13.8 1.0 CD A:GLU73 2.9 12.9 1.0 CG A:ASP101 3.3 12.2 1.0 CD A:GLU21 3.4 10.7 1.0 CG A:ASP104 3.5 11.2 1.0 CG A:ASP137 3.5 10.4 1.0 C A:VAL102 3.6 10.7 1.0 OD2 A:ASP101 3.8 14.8 1.0 OE1 A:GLU21 3.8 11.4 1.0 N A:VAL102 3.8 11.2 1.0 CA A:CA211 4.0 12.4 1.0 ND2 A:ASN105 4.0 12.2 1.0 OD2 A:ASP104 4.0 12.7 1.0 N A:ASP104 4.1 11.0 1.0 CB A:ASP137 4.2 11.3 1.0 CA A:ASP137 4.4 11.9 1.0 CA A:VAL102 4.4 11.8 1.0 CG A:GLU73 4.4 14.2 1.0 OD2 A:ASP137 4.5 11.1 1.0 CB A:ASP101 4.5 12.2 1.0 CA A:ASP101 4.6 11.2 1.0 N A:ASN103 4.6 10.9 1.0 CB A:ASP104 4.6 11.1 1.0 CA A:ASN103 4.7 11.5 1.0 C A:ASP101 4.7 11.6 1.0 CG A:GLU21 4.7 10.3 1.0 NE A:ARG72 4.7 14.1 1.0 NH2 A:ARG72 4.7 17.0 1.0 CB A:ARG72 4.7 12.3 1.0 CA A:ASP104 4.8 11.2 1.0 C A:ASN103 4.8 11.1 1.0 CG2 A:VAL102 4.9 12.8 1.0

Calcium binding site 3 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca213 b:10.4 occ:1.00 O A:GLY141 2.3 11.0 1.0 O A:ASN105 2.3 10.2 1.0 OD2 A:ASP186 2.4 10.9 1.0 OD1 A:ASN103 2.4 11.3 1.0 OD2 A:ASP135 2.4 11.5 1.0 OD2 A:ASP137 2.4 11.1 1.0 OD1 A:ASP135 2.5 11.5 1.0 CG A:ASP135 2.8 10.9 1.0 CG A:ASP186 3.4 9.8 1.0 CG A:ASN103 3.4 10.5 1.0 CG A:ASP137 3.4 10.4 1.0 C A:GLY141 3.5 11.0 1.0 C A:ASN105 3.5 10.2 1.0 CB A:ASP137 3.6 11.3 1.0 ND2 A:ASN103 3.8 12.5 1.0 CB A:ASP186 3.8 9.8 1.0 CA A:GLY141 4.2 12.1 1.0 N A:ASN105 4.2 10.8 1.0 CA A:ASN105 4.2 10.5 1.0 CB A:ASP135 4.3 11.2 1.0 CB A:ASN105 4.3 11.2 1.0 OD1 A:ASP186 4.4 11.3 1.0 N A:ALA106 4.5 9.9 1.0 N A:GLY142 4.5 11.5 1.0 OD1 A:ASP137 4.5 10.9 1.0 CA A:ALA106 4.6 9.9 1.0 CB A:ASN103 4.7 11.2 1.0 N A:ASP137 4.7 12.0 1.0 CA A:GLY142 4.8 12.1 1.0 CA A:ASP137 4.8 11.9 1.0 CD1 A:LEU193 4.9 12.9 1.0 C A:ALA106 4.9 9.9 1.0 CA A:ASN103 4.9 11.5 1.0

Calcium binding site 4 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca214 b:10.7 occ:1.00 OD1 A:ASP205 2.3 12.8 1.0 OD1 A:ASP208 2.4 13.7 1.0 O A:MET206 2.4 10.5 1.0 OE2 A:GLU173 2.4 17.9 1.0 OE2 A:GLU120 2.4 10.0 1.0 O A:HOH486 2.4 20.9 1.0 OE1 A:GLU173 2.8 14.7 1.0 CD A:GLU173 3.0 14.2 1.0 CG A:ASP208 3.3 13.4 1.0 CG A:ASP205 3.5 12.2 1.0 CD A:GLU120 3.5 9.4 1.0 C A:MET206 3.6 9.6 1.0 N A:MET206 3.8 9.6 1.0 OD2 A:ASP208 3.9 14.8 1.0 OE1 A:GLU120 3.9 9.8 1.0 CA A:CA215 4.0 12.6 1.0 N A:ASP208 4.1 12.8 1.0 OD2 A:ASP205 4.1 14.6 1.0 O A:HOH241 4.2 19.5 1.0 CA A:MET206 4.3 9.7 1.0 CB A:ASP208 4.4 14.0 1.0 C A:ASP205 4.4 9.4 1.0 CG A:GLU173 4.5 14.1 1.0 O A:HOH340 4.5 41.4 1.0 CA A:ASP205 4.5 9.8 1.0 C1 A:EDO236 4.5 28.5 1.0 CB A:ASP205 4.6 10.6 1.0 N A:GLN207 4.6 9.8 1.0 O1 A:EDO236 4.6 29.8 1.0 CB A:TYR172 4.7 9.1 1.0 O A:HOH303 4.7 38.3 1.0 CG A:GLU120 4.8 9.8 1.0 CA A:ASP208 4.8 13.8 1.0 CA A:GLN207 4.8 10.6 1.0 O A:HOH338 4.9 26.0 1.0 C A:GLN207 5.0 11.7 1.0 CD2 A:TYR172 5.0 10.4 1.0 CB A:MET206 5.0 9.9 1.0

Calcium binding site 5 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca215 b:12.6 occ:1.00 OE1 A:GLU173 2.3 14.7 1.0 O A:HOH338 2.3 26.0 1.0 OD1 A:ASP171 2.3 11.9 1.0 OE1 A:GLU120 2.4 9.8 1.0 O A:HOH485 2.4 18.3 1.0 OD2 A:ASP208 2.4 14.8 1.0 CG A:ASP208 3.2 13.4 1.0 OD1 A:ASP208 3.3 13.7 1.0 CD A:GLU120 3.3 9.4 1.0 CG A:ASP171 3.3 10.5 1.0 CD A:GLU173 3.5 14.2 1.0 OE2 A:GLU120 3.6 10.0 1.0 CA A:CA214 4.0 10.7 1.0 OD2 A:ASP171 4.0 13.5 1.0 CA A:ASP171 4.1 9.5 1.0 N A:TYR172 4.2 8.8 1.0 O A:HOH436 4.2 25.9 1.0 CB A:ASP171 4.2 10.5 1.0 OE2 A:GLU173 4.3 17.9 1.0 CG A:GLU173 4.4 14.1 1.0 O A:HOH367 4.4 19.9 1.0 N A:GLU173 4.4 10.8 1.0 O A:HOH340 4.4 41.4 1.0 CB A:GLU173 4.5 13.1 1.0 C A:ASP171 4.5 9.2 1.0 CG A:GLU120 4.6 9.8 1.0 CB A:ASP208 4.6 14.0 1.0 O A:HOH310 4.8 39.3 1.0 O A:HOH399 4.9 22.1 1.0

Calcium binding site 6 out of 6 in the Structure of the N-Terminus of Cadherin 23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the N-Terminus of Cadherin 23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca216 b:8.8 occ:1.00 O A:ARG4 2.3 9.7 1.0 OD2 A:ASP40 2.4 10.3 1.0 OD2 A:ASP38 2.4 11.6 1.0 OD1 A:ASN3 2.4 9.6 1.0 OD2 A:ASP86 2.4 9.1 1.0 OD1 A:ASP36 2.4 9.8 1.0 OD2 A:ASP36 2.6 11.1 1.0 CG A:ASP36 2.9 9.4 1.0 CG A:ASN3 3.4 10.4 1.0 CG A:ASP86 3.4 7.2 1.0 CG A:ASP38 3.4 11.5 1.0 C A:ARG4 3.5 9.9 1.0 CG A:ASP40 3.5 10.9 1.0 CB A:ASP86 3.7 7.9 1.0 ND2 A:ASN3 3.7 10.7 1.0 CB A:ASP38 3.8 11.9 1.0 N A:ARG4 3.9 10.7 1.0 CB A:ASP40 4.1 10.5 1.0 NE2 A:GLN88 4.2 13.9 1.0 CA A:ARG4 4.3 10.3 1.0 CB A:ASP36 4.4 9.7 1.0 N A:LEU5 4.4 10.5 1.0 OD1 A:ASP40 4.5 14.3 1.0 CA A:LEU5 4.5 10.7 1.0 OD1 A:ASP38 4.5 13.7 1.0 OD1 A:ASP86 4.6 7.7 1.0 N A:ASP38 4.6 10.9 1.0 CB A:ASN3 4.6 11.9 1.0 C A:LEU5 4.7 10.1 1.0 C2 A:EDO217 4.7 23.1 1.0 C A:ASN3 4.8 11.3 1.0 CA A:ASN3 4.8 12.0 1.0 CD A:PRO6 4.8 9.6 1.0 CA A:ASP38 4.8 11.5 1.0 N A:PRO6 4.8 9.3 1.0 CB A:ARG4 4.9 11.5 1.0

H.M.Elledge, P.Kazmierczak, P.Clark, J.S.Joseph, A.Kolatkar, P.Kuhn, U.Muller. Structure of the N Terminus of Cadherin 23 Reveals A New Adhesion Mechanism For A Subset of Cadherin Superfamily Members. Proc.Natl.Acad.Sci.Usa V. 107 10708 2010.
ISSN: ISSN 0027-8424
PubMed: 20498078
DOI: 10.1073/PNAS.1006284107