Calcium in PDB 5vvm: Crystal Structure of Human CDH23 EC21-23

The structure of Crystal Structure of Human CDH23 EC21-23, PDB code: 5vvm was solved by A.Patel, A.Jaiganesh, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.08 / 3.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.714, 166.806, 47.930, 90.00, 102.53, 90.00
R / Rfree (%)	30.3 / 34.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human CDH23 EC21-23 (pdb code 5vvm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Human CDH23 EC21-23, PDB code: 5vvm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2501 b:44.6 occ:1.00 OD1 A:ASN2224 2.3 43.4 1.0 OD2 A:ASP2265 2.5 42.0 1.0 OE1 A:GLU2162 2.6 43.0 1.0 OE1 A:GLU2226 3.1 42.6 1.0 OD1 A:ASP2265 3.1 41.7 1.0 CG A:ASP2265 3.1 41.9 1.0 CG A:ASN2224 3.2 44.3 1.0 CD A:GLU2162 3.5 43.4 1.0 ND2 A:ASN2266 3.7 40.7 1.0 OE2 A:GLU2162 3.7 43.4 1.0 ND2 A:ASN2224 4.0 44.7 1.0 CD A:GLU2226 4.2 42.8 1.0 CB A:ASN2224 4.2 45.3 1.0 CA A:CA2502 4.2 42.6 1.0 CA A:ASN2224 4.4 45.2 1.0 CB A:ASP2265 4.6 42.5 1.0 CG A:ASN2266 4.7 40.2 1.0 CG A:GLU2226 4.8 42.9 1.0 CG A:GLU2162 4.9 44.3 1.0 N A:ARG2225 4.9 45.1 1.0 CB A:GLU2226 4.9 44.0 1.0 OD1 A:ASN2266 4.9 40.3 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2502 b:42.6 occ:1.00 OD1 A:ASP2301 2.2 41.9 1.0 OD1 A:ASP2262 2.4 44.7 1.0 OE2 A:GLU2162 2.5 43.4 1.0 OE2 A:GLU2226 2.6 43.2 1.0 OD1 A:ASP2265 2.7 41.7 1.0 OE1 A:GLU2226 2.8 42.6 1.0 O A:VAL2263 2.8 43.6 1.0 CD A:GLU2226 3.0 42.8 1.0 CG A:ASP2301 3.3 42.2 1.0 CG A:ASP2262 3.5 46.0 1.0 CD A:GLU2162 3.5 43.4 1.0 OD2 A:ASP2262 3.9 46.4 1.0 OE1 A:GLU2162 3.9 43.0 1.0 CB A:ASP2301 3.9 43.6 1.0 ND2 A:ASN2266 3.9 40.7 1.0 C A:VAL2263 4.0 44.9 1.0 CG A:ASP2265 4.0 41.9 1.0 N A:VAL2263 4.1 45.7 1.0 CA A:CA2501 4.2 44.6 1.0 CA A:ASP2301 4.3 44.0 1.0 N A:ASP2265 4.3 42.6 1.0 CG A:GLU2226 4.4 42.9 1.0 NE A:ARG2225 4.4 46.5 1.0 OD2 A:ASP2301 4.4 41.6 1.0 CA A:VAL2263 4.7 45.9 1.0 CG A:GLU2162 4.7 44.3 1.0 CB A:ASP2262 4.7 47.7 1.0 OD2 A:ASP2265 4.7 42.0 1.0 CB A:ARG2225 4.8 45.7 1.0 CA A:ASP2262 4.9 47.2 1.0 N A:ASN2264 4.9 45.6 1.0 CA A:ASN2264 4.9 44.8 1.0 CB A:ASP2265 4.9 42.5 1.0 N A:ASN2266 4.9 40.7 1.0 NH2 A:ARG2225 5.0 46.5 1.0 C A:ASP2262 5.0 47.1 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2503 b:42.2 occ:1.00 OD1 A:ASP2299 2.1 41.7 1.0 OD2 A:ASP2301 2.3 41.6 1.0 OD1 A:ASN2264 2.3 44.0 1.0 O A:ASN2266 2.3 40.4 1.0 O A:ASN2305 2.4 45.1 1.0 OD2 A:ASP2353 2.6 44.1 1.0 CG A:ASP2299 2.8 41.4 1.0 OD2 A:ASP2299 2.9 41.0 1.0 CG A:ASP2301 3.3 42.2 1.0 CG A:ASN2264 3.4 45.3 1.0 C A:ASN2266 3.5 39.9 1.0 C A:ASN2305 3.5 46.6 1.0 CG A:ASP2353 3.6 45.1 1.0 CB A:ASP2353 3.7 45.1 1.0 CB A:ASP2301 3.8 43.6 1.0 ND2 A:ASN2264 4.0 46.1 1.0 N A:ASN2266 4.2 40.7 1.0 CA A:GLY2306 4.2 45.8 1.0 N A:GLY2306 4.3 47.0 1.0 OD1 A:ASP2301 4.3 41.9 1.0 CA A:ASN2266 4.3 40.0 1.0 CB A:ASP2299 4.4 41.8 1.0 N A:THR2267 4.5 39.7 1.0 CA A:ASN2305 4.5 48.4 1.0 CB A:ASN2305 4.5 47.4 1.0 CB A:ASN2264 4.6 46.2 1.0 OD1 A:ASP2353 4.7 46.4 1.0 CA A:THR2267 4.7 39.7 1.0 C A:ASN2264 4.8 43.8 1.0 CB A:ASN2266 4.8 39.9 1.0 CA A:ASN2264 4.8 44.8 1.0 N A:ASP2301 4.8 43.2 1.0 CD A:ARG2359 4.8 43.4 1.0 N A:ASP2265 4.9 42.6 1.0 CA A:ASP2301 4.9 44.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2504 b:59.7 occ:1.00 OE2 A:GLU2340 2.2 57.3 1.0 OD2 A:ASP2374 2.6 60.5 1.0 OD1 A:ASP2338 2.6 56.7 1.0 OE2 A:GLU2284 3.1 55.4 1.0 CG A:ASP2338 3.2 58.0 1.0 CG A:ASP2374 3.3 60.7 1.0 OD2 A:ASP2338 3.4 60.4 1.0 CD A:GLU2340 3.4 56.0 1.0 OD1 A:ASP2374 3.5 59.2 1.0 ND2 A:ASN2375 3.5 61.6 1.0 CD A:GLU2284 3.8 54.8 1.0 OE1 A:GLU2284 4.0 54.9 1.0 OE1 A:GLU2340 4.2 54.7 1.0 CG A:GLU2340 4.4 56.4 1.0 CB A:GLU2340 4.5 57.0 1.0 CB A:ASP2338 4.5 57.0 1.0 CA A:CA2505 4.6 55.5 1.0 CB A:ASP2374 4.7 63.2 1.0 CG A:ASN2375 4.8 62.6 1.0 CA A:ASP2338 4.9 54.6 1.0 N A:GLU2340 5.0 53.7 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2505 b:55.5 occ:1.00 OD1 A:ASP2407 2.3 57.4 1.0 OE1 A:GLU2284 2.3 54.9 1.0 OD1 A:ASP2371 2.3 53.8 1.0 OE1 A:GLU2340 2.4 54.7 1.0 O A:ILE2372 2.5 57.9 1.0 OD1 A:ASP2374 2.5 59.2 1.0 CG A:ASP2407 3.1 57.9 1.0 CD A:GLU2340 3.3 56.0 1.0 OE2 A:GLU2340 3.4 57.3 1.0 CD A:GLU2284 3.5 54.8 1.0 CG A:ASP2371 3.6 53.4 1.0 CG A:ASP2374 3.6 60.7 1.0 N A:ILE2372 3.6 55.1 1.0 C A:ILE2372 3.6 58.6 1.0 CB A:ASP2407 3.7 56.8 1.0 OD2 A:ASP2407 3.9 59.5 1.0 OD2 A:ASP2374 4.1 60.5 1.0 OE2 A:GLU2284 4.2 55.4 1.0 CA A:ILE2372 4.2 57.5 1.0 N A:ASP2374 4.3 62.4 1.0 CA A:ASP2407 4.3 56.2 1.0 OD2 A:ASP2371 4.3 54.0 1.0 CA A:ASP2371 4.4 52.1 1.0 C A:ASP2371 4.5 53.9 1.0 ND2 A:ASN2375 4.5 61.6 1.0 CB A:ASP2371 4.6 52.3 1.0 CG A:GLU2284 4.6 54.4 1.0 CG A:GLU2340 4.6 56.4 1.0 CA A:CA2504 4.6 59.7 1.0 CB A:ASP2374 4.7 63.2 1.0 CB A:TYR2339 4.7 50.6 1.0 N A:ASN2373 4.7 60.6 1.0 CG1 A:ILE2372 4.8 58.5 1.0 CA A:ASP2374 4.9 64.1 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Human CDH23 EC21-23


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 Human CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2506 b:61.7 occ:1.00 OD1 A:ASN2373 2.2 63.1 1.0 OD2 A:ASP2407 2.2 59.5 1.0 OD1 A:ASP2405 2.3 61.1 1.0 O A:ASN2375 2.6 64.8 1.0 O A:PHE2411 2.7 60.8 1.0 OD2 A:ASP2405 2.7 63.6 1.0 CG A:ASP2405 2.9 62.3 1.0 OD2 A:ASP2456 3.1 66.6 1.0 CG A:ASP2407 3.3 57.9 1.0 CG A:ASN2373 3.3 64.7 1.0 CB A:ASP2407 3.7 56.8 1.0 C A:ASN2375 3.7 65.9 1.0 C A:PHE2411 3.8 60.3 1.0 CG A:ASP2456 3.9 67.2 1.0 CB A:PHE2411 3.9 59.1 1.0 ND2 A:ASN2373 4.1 67.3 1.0 N A:ASN2375 4.1 63.8 1.0 CB A:ASP2456 4.2 66.1 1.0 CA A:ASN2373 4.2 62.0 1.0 CB A:ASN2375 4.2 62.7 1.0 CA A:ASN2375 4.3 64.7 1.0 CA A:PHE2411 4.3 60.4 1.0 CB A:ASN2373 4.3 64.0 1.0 CB A:ASP2405 4.3 62.5 1.0 OD1 A:ASP2407 4.4 57.4 1.0 C A:ASN2373 4.6 63.5 1.0 N A:ASP2374 4.7 62.4 1.0 N A:ASP2407 4.7 57.6 1.0 CA A:ASP2407 4.8 56.2 1.0 OD1 A:ASP2456 4.8 69.0 1.0 N A:ASN2376 4.8 68.4 1.0 N A:ALA2412 4.9 60.1 1.0 CG A:PHE2411 4.9 59.5 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Human CDH23 EC21-23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2501 b:43.7 occ:1.00 OE1 B:GLU2162 2.3 43.1 1.0 OD1 B:ASP2265 2.3 41.1 1.0 OD2 B:ASP2265 2.5 41.5 1.0 OE1 B:GLU2226 2.5 42.2 1.0 CG B:ASP2265 2.7 41.3 1.0 OD1 B:ASN2224 3.0 43.5 1.0 OE2 B:GLU2162 3.0 43.2 1.0 CD B:GLU2162 3.0 43.5 1.0 ND2 B:ASN2266 3.3 40.0 1.0 CA B:CA2502 3.4 41.8 1.0 CD B:GLU2226 3.6 42.0 1.0 CG B:ASN2224 3.6 44.0 1.0 ND2 B:ASN2224 3.9 43.7 1.0 CB B:ASP2265 4.2 41.6 1.0 OE2 B:GLU2226 4.3 42.2 1.0 CG B:GLU2226 4.4 42.0 1.0 CG B:ASN2266 4.4 39.4 1.0 CG B:GLU2162 4.5 44.6 1.0 OD1 B:ASP2301 4.6 40.7 1.0 O B:VAL2263 4.6 42.5 1.0 CB B:ASN2224 4.7 45.2 1.0 CB B:GLU2226 4.7 43.1 1.0 N B:ARG2225 4.8 45.2 1.0 CA B:ASN2224 4.8 45.4 1.0 N B:GLU2226 4.9 44.5 1.0 CG2 B:VAL2263 4.9 43.9 1.0 OD1 B:ASN2266 5.0 39.6 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Human CDH23 EC21-23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2502 b:41.8 occ:1.00 OD1 B:ASP2301 2.1 40.7 1.0 OD1 B:ASP2262 2.3 43.5 1.0 OE2 B:GLU2162 2.6 43.2 1.0 O B:VAL2263 2.7 42.5 1.0 OE2 B:GLU2226 2.7 42.2 1.0 OD1 B:ASP2265 2.8 41.1 1.0 OE1 B:GLU2226 2.9 42.2 1.0 CD B:GLU2226 3.1 42.0 1.0 CG B:ASP2301 3.2 40.5 1.0 CG B:ASP2262 3.3 44.5 1.0 CA B:CA2501 3.4 43.7 1.0 CD B:GLU2162 3.6 43.5 1.0 OD2 B:ASP2262 3.8 44.4 1.0 CB B:ASP2301 3.8 41.5 1.0 C B:VAL2263 3.8 43.5 1.0 CG B:ASP2265 4.0 41.3 1.0 OE1 B:GLU2162 4.0 43.1 1.0 N B:VAL2263 4.1 44.8 1.0 ND2 B:ASN2266 4.1 40.0 1.0 N B:ASP2265 4.2 41.2 1.0 CA B:ASP2301 4.2 42.0 1.0 OD2 B:ASP2301 4.3 39.9 1.0 NE B:ARG2225 4.4 45.2 1.0 CG B:GLU2226 4.5 42.0 1.0 CA B:VAL2263 4.6 44.7 1.0 CB B:ASP2262 4.6 46.0 1.0 CA B:ASN2264 4.7 42.6 1.0 N B:ASN2264 4.7 43.7 1.0 CG B:GLU2162 4.8 44.6 1.0 CA B:ASP2262 4.8 46.2 1.0 CG2 B:VAL2263 4.8 43.9 1.0 OD2 B:ASP2265 4.8 41.5 1.0 N B:ASN2266 4.9 39.5 1.0 CB B:ASP2265 4.9 41.6 1.0 C B:ASP2262 4.9 46.0 1.0 CB B:ARG2225 4.9 45.4 1.0 CA B:ASP2265 5.0 41.0 1.0 C B:ASN2264 5.0 41.9 1.0 N B:ASP2301 5.0 41.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Human CDH23 EC21-23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2503 b:39.7 occ:1.00 O B:ASN2266 2.1 38.6 1.0 OD1 B:ASN2264 2.3 41.4 1.0 OD1 B:ASP2299 2.3 39.4 1.0 OD2 B:ASP2301 2.4 39.9 1.0 OD2 B:ASP2353 2.5 40.8 1.0 O B:ASN2305 2.7 41.8 1.0 OD2 B:ASP2299 2.8 38.5 1.0 CG B:ASP2299 2.9 38.9 1.0 C B:ASN2266 3.3 38.4 1.0 CG B:ASN2264 3.4 42.4 1.0 CG B:ASP2353 3.5 41.3 1.0 CG B:ASP2301 3.5 40.5 1.0 CB B:ASP2353 3.7 41.2 1.0 C B:ASN2305 3.9 42.9 1.0 ND2 B:ASN2264 3.9 42.8 1.0 CB B:ASP2301 4.1 41.5 1.0 N B:ASN2266 4.1 39.5 1.0 CA B:ASN2266 4.2 38.8 1.0 N B:THR2267 4.3 38.2 1.0 CA B:THR2267 4.4 38.0 1.0 OD1 B:ASP2301 4.5 40.7 1.0 CB B:ASP2299 4.5 39.1 1.0 CA B:GLY2306 4.5 42.0 1.0 OD1 B:ASP2353 4.6 42.1 1.0 CB B:ASN2264 4.6 43.4 1.0 N B:GLY2306 4.6 43.1 1.0 C B:ASN2264 4.6 41.9 1.0 CB B:ASN2266 4.7 38.8 1.0 CA B:ASN2264 4.8 42.6 1.0 CB B:ASN2305 4.8 44.1 1.0 CA B:ASN2305 4.8 44.4 1.0 N B:ASP2265 4.8 41.2 1.0 O B:ASN2264 4.9 42.2 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Human CDH23 EC21-23


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human CDH23 EC21-23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2504 b:56.2 occ:1.00 OE2 B:GLU2340 2.2 55.6 1.0 OD1 B:ASP2338 2.5 53.7 1.0 OD2 B:ASP2374 2.6 57.1 1.0 OE2 B:GLU2284 2.9 52.8 1.0 CG B:ASP2338 3.1 54.1 1.0 OD2 B:ASP2338 3.3 55.9 1.0 CG B:ASP2374 3.4 57.9 1.0 CD B:GLU2340 3.4 55.0 1.0 OD1 B:ASP2374 3.5 57.4 1.0 ND2 B:ASN2375 3.7 59.6 1.0 CD B:GLU2284 3.7 52.8 1.0 OE1 B:GLU2284 3.9 53.5 1.0 OE1 B:GLU2340 4.2 54.4 1.0 CB B:ASP2338 4.4 52.8 1.0 CG B:GLU2340 4.4 55.6 1.0 CB B:GLU2340 4.5 55.3 1.0 CA B:CA2505 4.7 55.2 1.0 CB B:ASP2374 4.7 59.9 1.0 CA B:ASP2338 4.7 51.1 1.0 N B:GLU2340 4.9 52.4 1.0 CG B:ASN2375 4.9 61.0 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