Calcium in PDB 1l3w: C-Cadherin Ectodomain

The structure of C-Cadherin Ectodomain, PDB code: 1l3w was solved by T.J.Boggon, J.Murray, S.Chappuis-Flament, E.Wong, B.M.Gumbiner, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.166, 75.135, 129.813, 90.00, 105.50, 90.00
R / Rfree (%)	24.3 / 27.6

Pages:

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

Binding sites:

The binding sites of Calcium atom in the C-Cadherin Ectodomain (pdb code 1l3w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the C-Cadherin Ectodomain, PDB code: 1l3w:
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 C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:22.4 occ:1.00 OD2 A:ASP134 2.1 51.6 1.0 O A:ASN104 2.3 47.5 1.0 O A:ASN143 2.3 41.2 1.0 OD1 A:ASP134 2.6 51.6 1.0 CG A:ASP134 2.7 51.6 1.0 OD2 A:ASP136 2.8 42.7 1.0 OD2 A:ASP195 2.8 34.4 1.0 OD1 A:ASN102 2.8 55.7 1.0 OD1 A:ASP195 2.9 34.4 1.0 CG A:ASP195 3.2 34.4 1.0 C A:ASN104 3.4 47.5 1.0 C A:ASN143 3.5 41.2 1.0 CG A:ASP136 3.7 42.7 1.0 CB A:ASP136 3.8 42.7 1.0 CG A:ASN102 3.8 55.7 1.0 CA A:ASN104 4.1 47.5 1.0 CB A:ASP134 4.2 51.6 1.0 N A:ASN104 4.2 47.5 1.0 CA A:ASN143 4.2 41.2 1.0 CB A:ASN104 4.2 79.0 1.0 ND2 A:ASN102 4.5 55.7 1.0 CB A:ASN143 4.5 34.4 1.0 N A:GLY144 4.5 31.3 1.0 N A:ARG105 4.6 90.2 1.0 CB A:ASP195 4.7 34.4 1.0 CA A:GLY144 4.7 31.3 1.0 CA A:ASN102 4.8 33.5 1.0 N A:ASP136 4.8 14.1 1.0 OD1 A:ASP136 4.8 42.7 1.0 CA A:ARG105 4.9 90.2 1.0 CB A:ASN102 4.9 55.7 1.0 CA A:ASP136 4.9 14.1 1.0

Calcium binding site 2 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:5.0 occ:1.00 OD1 A:ASP136 2.2 42.7 1.0 O A:GLN101 2.2 43.4 1.0 OE2 A:GLU69 2.3 15.8 1.0 OD2 A:ASP103 2.5 33.9 1.0 OE1 A:GLU11 2.7 21.0 1.0 OD2 A:ASP100 3.0 34.3 1.0 CD A:GLU69 3.0 15.8 1.0 OD1 A:ASP103 3.0 33.9 1.0 OE1 A:GLU69 3.0 15.8 1.0 CG A:ASP103 3.0 33.9 1.0 OD1 A:ASP100 3.1 34.3 1.0 CG A:ASP100 3.1 34.3 1.0 CG A:ASP136 3.2 42.7 1.0 N A:GLN101 3.3 43.4 1.0 C A:GLN101 3.3 43.4 1.0 OE2 A:GLU11 3.5 21.0 1.0 CD A:GLU11 3.5 21.0 1.0 CA A:GLN101 3.9 43.4 1.0 CB A:ASP136 3.9 42.7 1.0 OD2 A:ASP136 4.0 42.7 1.0 N A:ASP103 4.1 73.5 1.0 NE A:ARG68 4.1 39.4 1.0 CD A:ARG68 4.1 39.4 1.0 CG A:ARG68 4.1 39.4 1.0 CB A:ASP100 4.2 34.3 1.0 CA A:ASP136 4.3 14.1 1.0 C A:ASP100 4.3 42.9 1.0 CA A:ASP100 4.3 42.9 1.0 CG A:GLU69 4.4 15.8 1.0 N A:ASN102 4.4 33.5 1.0 CB A:ASP103 4.4 33.9 1.0 CA A:CA602 4.5 15.4 1.0 CB A:GLN101 4.6 71.4 1.0 ND2 A:ASN104 4.7 79.0 1.0 CA A:ASN102 4.8 33.5 1.0 CA A:ASP103 4.8 73.5 1.0 C A:ASN102 4.9 33.5 1.0 CG A:GLU11 5.0 21.0 1.0

Calcium binding site 3 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:15.4 occ:1.00 OD2 A:ASP67 2.2 32.7 1.0 OD1 A:ASP103 2.3 33.9 1.0 OE1 A:GLU69 2.4 15.8 1.0 OE2 A:GLU11 2.7 21.0 1.0 CG A:ASP103 2.9 33.9 1.0 CG A:ASP67 2.9 32.7 1.0 OD1 A:ASN12 3.3 43.9 1.0 CD A:GLU11 3.3 21.0 1.0 OD2 A:ASP103 3.5 33.9 1.0 OD1 A:ASP67 3.6 32.7 1.0 CB A:ASP103 3.6 33.9 1.0 CD A:GLU69 3.6 15.8 1.0 CB A:ASP67 3.8 32.7 1.0 ND2 A:ASN12 3.8 43.9 1.0 CG A:ASN12 3.9 43.9 1.0 CG A:GLU11 4.0 21.0 1.0 OE1 A:GLU11 4.0 21.0 1.0 CA A:ASP67 4.2 43.9 1.0 CG A:GLU69 4.4 15.8 1.0 CB A:GLU69 4.5 15.8 1.0 CA A:CA601 4.5 5.0 1.0 OE2 A:GLU69 4.6 15.8 1.0 O A:HOH1009 4.7 24.3 1.0 C A:ASP67 4.9 43.9 1.0 ND2 A:ASN104 4.9 79.0 1.0 N A:ARG68 5.0 51.6 1.0 N A:GLU69 5.0 33.9 1.0

Calcium binding site 4 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:10.5 occ:1.00 OD2 A:ASP248 2.2 28.0 1.0 O A:ALA214 2.3 30.5 1.0 OE1 A:GLU182 2.4 17.1 1.0 OD1 A:ASP216 2.5 10.1 1.0 OD1 A:ASP213 2.7 47.1 1.0 OE2 A:GLU119 2.7 8.7 1.0 CD A:GLU182 2.7 17.1 1.0 OD2 A:ASP213 2.9 47.1 1.0 CG A:ASP213 3.0 47.1 1.0 CG A:ASP248 3.1 28.0 1.0 OE2 A:GLU182 3.2 17.1 1.0 C A:ALA214 3.5 30.5 1.0 CB A:ASP248 3.5 28.0 1.0 N A:ALA214 3.6 30.5 1.0 CG A:GLU182 3.6 17.1 1.0 CG A:ASP216 3.7 10.1 1.0 CA A:ASP248 3.8 22.1 1.0 CD A:GLU119 3.8 8.7 1.0 NE A:ARG181 4.0 47.9 1.0 ND2 A:ASN217 4.0 53.4 1.0 CA A:ALA214 4.1 30.5 1.0 OD1 A:ASP248 4.1 28.0 1.0 OE1 A:GLU119 4.1 8.7 1.0 N A:ASP216 4.2 48.2 1.0 CB A:ASP216 4.4 10.1 1.0 CB A:ASP213 4.4 47.1 1.0 C A:ASP213 4.6 43.1 1.0 OD2 A:ASP216 4.6 10.1 1.0 N A:ASN215 4.6 34.3 1.0 CA A:ASP213 4.6 43.1 1.0 N A:ASP248 4.7 22.1 1.0 CD A:ARG181 4.7 47.9 1.0 NH2 A:ARG181 4.7 47.9 1.0 CB A:ALA214 4.8 30.5 1.0 CB A:ARG181 4.8 47.9 1.0 CA A:CA604 4.8 12.9 1.0 C A:ASP248 4.8 22.1 1.0 CZ A:ARG181 4.8 47.9 1.0 CA A:ASP216 4.9 48.2 1.0 N A:MET249 4.9 41.8 1.0 CA A:ASN215 4.9 34.3 1.0

Calcium binding site 5 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:12.9 occ:1.00 OD1 A:ASP180 2.2 24.0 1.0 OE2 A:GLU182 2.3 17.1 1.0 OD2 A:ASP216 2.4 10.1 1.0 OE1 A:GLU119 2.5 8.7 1.0 CG A:ASP216 2.6 10.1 1.0 CG A:ASP180 2.8 24.0 1.0 CD A:GLU182 3.0 17.1 1.0 CB A:ASP216 3.1 10.1 1.0 OE1 A:GLU182 3.2 17.1 1.0 OD1 A:ASP216 3.2 10.1 1.0 OD2 A:ASP180 3.3 24.0 1.0 CD A:GLU119 3.5 8.7 1.0 CB A:ASP180 3.6 24.0 1.0 CA A:ASP180 3.9 28.1 1.0 OE2 A:GLU119 4.1 8.7 1.0 CG A:GLU182 4.2 17.1 1.0 CB A:GLU182 4.4 17.1 1.0 N A:ARG181 4.5 27.8 1.0 ND2 A:ASN217 4.6 53.4 1.0 O A:LEU179 4.6 22.6 1.0 C A:ASP180 4.6 28.1 1.0 CA A:ASP216 4.6 48.2 1.0 CG A:GLU119 4.6 8.7 1.0 N A:GLU182 4.6 40.6 1.0 CA A:CA603 4.8 10.5 1.0

Calcium binding site 6 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:10.5 occ:1.00 O A:ASN217 2.3 65.3 1.0 OD1 A:ASP248 2.4 28.0 1.0 OD1 A:ASN215 2.4 28.6 1.0 OD1 A:ASN304 2.5 57.1 1.0 OD2 A:ASP246 2.5 13.3 1.0 OD1 A:ASP246 2.7 13.3 1.0 O A:ALA254 2.7 24.4 1.0 CG A:ASP246 2.9 13.3 1.0 C A:ASN217 3.3 65.3 1.0 CG A:ASP248 3.4 28.0 1.0 CG A:ASN215 3.5 28.6 1.0 CG A:ASN304 3.7 57.1 1.0 C A:ALA254 3.7 24.4 1.0 CB A:ASP248 3.9 28.0 1.0 CA A:ASN217 4.0 65.3 1.0 CA A:ALA254 4.1 24.4 1.0 CB A:ALA254 4.1 24.4 1.0 N A:ASN217 4.2 65.3 1.0 ND2 A:ASN215 4.2 28.6 1.0 ND2 A:ASN304 4.2 57.1 1.0 CB A:ASN217 4.3 53.4 1.0 N A:ALA218 4.3 45.7 1.0 CA A:ASN215 4.4 34.3 1.0 CB A:ASP246 4.5 13.3 1.0 OD2 A:ASP248 4.5 28.0 1.0 CB A:ASN215 4.5 28.6 1.0 CA A:ALA218 4.6 45.7 1.0 C A:ASN215 4.6 34.3 1.0 N A:ASP248 4.7 22.1 1.0 O A:ASN215 4.8 34.3 1.0 N A:TRP255 4.8 50.6 1.0 CB A:ASN304 4.9 57.1 1.0 C A:ALA218 4.9 45.7 1.0 CA A:ASP248 5.0 22.1 1.0

Calcium binding site 7 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:37.4 occ:1.00 OE2 A:GLU291 2.0 52.9 1.0 OE2 A:GLU232 2.1 49.7 1.0 CD A:GLU232 2.7 49.7 1.0 OD2 A:ASP289 2.9 99.7 1.0 O A:ASP289 2.9 0.0 1.0 OE1 A:GLU232 2.9 49.7 1.0 OE2 A:GLU328 2.9 0.0 1.0 CD A:GLU291 3.1 52.9 1.0 C A:ASP289 3.5 0.0 1.0 OE1 A:GLU291 3.6 52.9 1.0 CA A:CA610 3.7 70.2 1.0 CA A:PHE290 3.8 52.9 1.0 CD A:GLU328 3.8 0.0 1.0 OE1 A:GLU328 3.9 0.0 1.0 CG A:GLU232 3.9 49.7 1.0 N A:PHE290 4.0 52.9 1.0 CG A:ASP289 4.0 99.7 1.0 N A:GLU291 4.2 99.8 1.0 CA A:ASP289 4.3 0.0 1.0 C A:PHE290 4.3 52.9 1.0 CG A:GLU291 4.4 52.9 1.0 CB A:GLU291 4.5 52.9 1.0 CB A:PHE290 4.6 99.0 1.0 CB A:ASP289 4.8 99.7 1.0 OD1 A:ASP289 4.9 99.7 1.0

Calcium binding site 8 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:90.9 occ:1.00 OD1 A:ASN327 2.0 0.0 1.0 O A:GLU328 2.3 0.0 1.0 OD2 A:ASP414 2.5 82.2 1.0 OE1 A:GLN365 2.6 0.0 1.0 OD2 A:ASP358 2.6 96.2 1.0 OD1 A:ASP360 2.8 90.8 1.0 CG A:ASP414 2.8 82.2 1.0 OD1 A:ASP414 2.9 82.2 1.0 CG A:ASN327 3.1 0.0 1.0 OD1 A:ASP358 3.2 96.2 1.0 CG A:ASP358 3.3 96.2 1.0 C A:GLU328 3.3 0.0 1.0 CD A:GLN365 3.5 0.0 1.0 ND2 A:ASN327 3.6 0.0 1.0 NE2 A:GLN365 3.7 0.0 1.0 N A:GLU328 3.8 0.0 1.0 CB A:ASP414 3.9 82.2 1.0 CG A:ASP360 3.9 90.8 1.0 C A:ASN327 4.0 0.0 1.0 CA A:GLU328 4.0 0.0 1.0 CB A:ASN327 4.3 0.0 1.0 N A:ALA329 4.3 93.5 1.0 O A:ASN327 4.4 0.0 1.0 CA A:ASN327 4.5 0.0 1.0 CA A:ALA329 4.6 93.5 1.0 OD2 A:ASP360 4.6 90.8 1.0 CB A:ASP358 4.7 96.2 1.0 O A:VAL419 4.8 0.0 1.0 CB A:ASP360 4.8 90.8 1.0 CG A:GLN365 4.8 0.0 1.0 C A:ALA329 4.8 93.5 1.0 CG A:PRO359 4.9 92.7 1.0

Calcium binding site 9 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:34.6 occ:1.00 OD2 A:ASP395 2.1 88.0 1.0 CG A:ASP395 2.4 88.0 1.0 OE1 A:GLU397 2.4 75.5 1.0 OD1 A:ASP435 2.5 64.9 1.0 OE2 A:GLU343 2.6 72.9 1.0 OD2 A:ASP435 2.7 64.9 1.0 OD1 A:ASP395 2.7 88.0 1.0 CG A:ASP435 2.7 64.9 1.0 OE1 A:GLU343 2.8 72.9 1.0 CD A:GLU343 3.0 72.9 1.0 CD A:GLU397 3.3 75.5 1.0 CB A:GLU397 3.5 75.5 1.0 CB A:ASP395 3.5 88.0 1.0 CG A:GLU397 3.6 75.5 1.0 CA A:CA611 3.7 85.4 1.0 CA A:ASP395 3.7 76.5 1.0 CB A:ASP435 3.8 64.9 1.0 N A:GLU397 3.8 0.0 1.0 C A:ASP395 4.0 76.5 1.0 N A:ARG396 4.1 89.7 1.0 CA A:GLU397 4.3 0.0 1.0 OE2 A:GLU397 4.4 75.5 1.0 CG A:GLU343 4.4 72.9 1.0 O A:ASP395 4.7 76.5 1.0 C A:ARG396 4.9 89.7 1.0

Calcium binding site 10 out of 12 in the C-Cadherin Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of C-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:69.9 occ:1.00 OD1 A:ASP461 2.3 0.0 1.0 OD2 A:ASP515 2.3 0.0 1.0 OD1 A:ASN434 2.3 68.5 1.0 OD1 A:ASP463 2.4 90.9 1.0 O A:ASN436 2.7 56.8 1.0 O A:ASN467 3.0 44.5 1.0 CG A:ASN434 3.0 68.5 1.0 CG A:ASP461 3.1 0.0 1.0 ND2 A:ASN434 3.2 68.5 1.0 OD2 A:ASP461 3.3 0.0 1.0 CG A:ASP463 3.3 90.9 1.0 CG A:ASP515 3.5 0.0 1.0 CB A:ASP463 3.6 90.9 1.0 C A:ASN436 3.6 56.8 1.0 OD1 A:ASP515 4.1 0.0 1.0 CA A:GLY437 4.1 93.1 1.0 C A:ASN467 4.2 44.5 1.0 N A:GLY437 4.2 93.1 1.0 CB A:ASP461 4.3 0.0 1.0 CB A:ASN434 4.4 68.5 1.0 OD2 A:ASP463 4.5 90.9 1.0 CB A:ASN467 4.6 73.4 1.0 CB A:ASP515 4.7 0.0 1.0 CG2 A:THR468 4.7 0.0 1.0 CA A:ASN436 4.7 56.8 1.0 N A:ASP463 4.8 0.0 1.0 CA A:ASN434 4.8 0.0 1.0 CA A:ASP463 4.8 0.0 1.0 N A:ASN436 4.8 56.8 1.0 C A:ASN434 4.9 0.0 1.0 C A:GLY437 4.9 93.1 1.0 CD A:PRO438 4.9 75.9 1.0 CA A:ASN467 4.9 44.5 1.0 O A:ASP435 5.0 99.6 1.0 C A:ASP435 5.0 99.6 1.0

T.J.Boggon, J.Murray, S.Chappuis-Flament, E.Wong, B.M.Gumbiner, L.Shapiro. C-Cadherin Ectodomain Structure and Implications For Cell Adhesion Mechanisms Science V. 296 1308 2002.
ISSN: ISSN 0036-8075
PubMed: 11964443
DOI: 10.1126/SCIENCE.1071559