Calcium in PDB 3q2v: Crystal Structure of Mouse E-Cadherin Ectodomain

The structure of Crystal Structure of Mouse E-Cadherin Ectodomain, PDB code: 3q2v was solved by X.Jin, O.J.Harrison, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.140, 79.697, 176.001, 90.00, 98.56, 90.00
R / Rfree (%)	23 / 29.3

The structure of Crystal Structure of Mouse E-Cadherin Ectodomain also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse E-Cadherin Ectodomain (pdb code 3q2v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of Mouse E-Cadherin Ectodomain, PDB code: 3q2v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:41.8 occ:1.00 OE1 A:GLU69 2.3 35.3 1.0 OD1 A:ASP103 2.7 46.9 1.0 OD1 A:ASP67 2.9 58.8 1.0 OE2 A:GLU11 2.9 51.5 1.0 OD2 A:ASP67 3.1 44.1 1.0 OE1 A:GLU11 3.2 54.5 1.0 CG A:ASP67 3.2 54.4 1.0 CD A:GLU11 3.4 55.4 1.0 CG A:ASP103 3.4 46.4 1.0 CD A:GLU69 3.5 37.5 1.0 OD1 A:ASN12 3.6 44.4 1.0 OD2 A:ASP103 3.8 48.5 1.0 OD1 A:ASN104 4.0 42.9 1.0 CG A:GLU69 4.1 40.2 1.0 CB A:GLU69 4.2 43.4 1.0 CA A:CA602 4.2 35.5 1.0 CB A:ASP67 4.4 56.9 1.0 OE2 A:GLU69 4.4 36.5 1.0 N A:GLU69 4.4 43.3 1.0 CG A:ASN12 4.5 59.7 1.0 ND2 A:ASN12 4.5 71.4 1.0 CB A:ASP103 4.6 41.9 1.0 N A:ARG68 4.6 43.8 1.0 CG A:GLU11 4.8 51.7 1.0 CA A:ASP67 4.8 47.2 1.0 CA A:GLU69 5.0 44.5 1.0

Calcium binding site 2 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:35.5 occ:1.00 O A:GLN101 2.5 46.7 1.0 OE1 A:GLU11 2.5 54.5 1.0 OD2 A:ASP100 2.5 49.7 1.0 OD2 A:ASP103 2.6 48.5 1.0 OE2 A:GLU69 2.6 36.5 1.0 OE1 A:GLU69 2.9 35.3 1.0 CD A:GLU69 3.1 37.5 1.0 OD1 A:ASP136 3.1 40.2 1.0 CG A:ASP100 3.2 51.2 1.0 CG A:ASP103 3.2 46.4 1.0 OD1 A:ASP103 3.3 46.9 1.0 N A:GLN101 3.4 46.9 1.0 OD1 A:ASP100 3.4 54.3 1.0 CG A:ASP136 3.5 40.0 1.0 C A:GLN101 3.5 51.0 1.0 CD A:GLU11 3.5 55.4 1.0 CA A:GLN101 4.0 53.1 1.0 CB A:ASP136 4.0 38.5 1.0 OD2 A:ASP136 4.0 42.6 1.0 OE2 A:GLU11 4.2 51.5 1.0 CA A:CA601 4.2 41.8 1.0 CA A:ASP136 4.2 37.7 1.0 OD1 A:ASN104 4.3 42.9 1.0 NH1 A:ARG68 4.3 40.1 1.0 C A:ASP100 4.4 46.2 1.0 CB A:ASP100 4.4 42.6 1.0 CA A:ASP100 4.4 45.7 1.0 N A:ASP103 4.5 42.6 1.0 CG A:GLU69 4.5 40.2 1.0 CG A:GLU11 4.5 51.7 1.0 CB A:GLN101 4.6 53.3 1.0 CB A:ASP103 4.6 41.9 1.0 N A:ASN102 4.6 54.0 1.0 CD A:ARG68 4.9 45.0 1.0 CB A:ARG68 5.0 44.3 1.0 CA A:ASN102 5.0 49.5 1.0

Calcium binding site 3 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:39.1 occ:1.00 OD1 A:ASN102 2.5 51.0 1.0 O A:ASN143 2.6 42.5 1.0 OD2 A:ASP136 2.7 42.6 1.0 OD1 A:ASP134 2.7 36.4 1.0 O A:ASN104 2.7 55.5 1.0 OD2 A:ASP134 2.8 34.1 1.0 OD1 A:ASP195 2.8 45.7 1.0 CG A:ASP134 3.1 36.5 1.0 CG A:ASP195 3.3 51.4 1.0 C A:ASN104 3.3 48.1 1.0 CG A:ASP136 3.5 40.0 1.0 C A:ASN143 3.7 43.7 1.0 CG A:ASN102 3.7 48.3 1.0 N A:ASN104 3.7 42.8 1.0 OD2 A:ASP195 3.9 45.9 1.0 CB A:ASP195 4.0 52.2 1.0 CA A:ASN104 4.0 40.1 1.0 CB A:ASP136 4.1 38.5 1.0 N A:ARG105 4.1 42.9 1.0 OD1 A:ASP136 4.3 40.2 1.0 CA A:ASN143 4.3 43.5 1.0 N A:ASP103 4.3 42.6 1.0 CB A:ASN143 4.4 44.6 1.0 CA A:ASN102 4.4 49.5 1.0 CB A:ASN104 4.4 39.4 1.0 CD1 A:LEU201 4.4 42.2 1.0 CA A:ARG105 4.5 46.6 1.0 CB A:ASN102 4.5 55.9 1.0 C A:ASN102 4.5 44.5 1.0 CB A:ASP134 4.6 39.9 1.0 ND2 A:ASN102 4.7 45.6 1.0 N A:ALA144 4.8 38.2 1.0 C A:ARG105 4.9 44.1 1.0 C A:ASP103 4.9 46.9 1.0

Calcium binding site 4 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:35.8 occ:1.00 OD1 A:ASP216 2.3 33.1 1.0 OD1 A:ASP180 2.4 40.1 1.0 OE2 A:GLU119 2.7 27.0 1.0 CG A:ASP180 3.1 38.4 1.0 OE2 A:GLU182 3.2 34.5 1.0 OD2 A:ASP180 3.4 47.3 1.0 CD A:GLU119 3.5 34.2 1.0 CG A:ASP216 3.5 43.4 1.0 CG A:GLU119 4.0 38.2 1.0 CB A:ASP180 4.1 32.2 1.0 CB A:ASP216 4.3 43.0 1.0 CA A:ASP180 4.3 36.1 1.0 OE1 A:GLU119 4.3 31.1 1.0 OD2 A:ASP216 4.4 41.2 1.0 CD A:GLU182 4.5 39.1 1.0 N A:ARG181 4.9 32.4 1.0 CB A:GLU182 5.0 39.1 1.0 O A:LEU179 5.0 38.6 1.0

Calcium binding site 5 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:31.7 occ:1.00 O A:ILE214 2.3 49.0 1.0 OE1 A:GLU182 2.4 35.9 1.0 OD2 A:ASP216 2.5 41.2 1.0 OD1 A:ASP213 2.6 50.8 1.0 OE1 A:GLU119 2.7 31.1 1.0 OD2 A:ASP248 2.8 44.4 1.0 CG A:ASP213 3.3 53.6 1.0 N A:ILE214 3.3 44.9 1.0 CD A:GLU182 3.4 39.1 1.0 CG A:ASP216 3.4 43.4 1.0 C A:ILE214 3.4 47.3 1.0 CD A:GLU119 3.5 34.2 1.0 OE2 A:GLU182 3.6 34.5 1.0 OD2 A:ASP213 3.6 53.6 1.0 CG A:ASP248 3.7 49.8 1.0 OE2 A:GLU119 3.7 27.0 1.0 CB A:ASP248 3.9 41.5 1.0 OD1 A:ASP216 4.0 33.1 1.0 N A:ASP216 4.0 42.7 1.0 CA A:ILE214 4.1 38.8 1.0 CD A:ARG181 4.1 40.8 1.0 CA A:ASP213 4.2 37.8 1.0 CA A:ASP248 4.2 39.7 1.0 C A:ASP213 4.3 43.5 1.0 CB A:ASP213 4.3 40.7 1.0 CB A:ASP216 4.3 43.0 1.0 CG2 A:ILE214 4.4 39.1 1.0 N A:ASN215 4.5 47.9 1.0 NH1 A:ARG181 4.6 47.5 1.0 OD1 A:ASP248 4.7 46.1 1.0 CG A:GLU182 4.7 37.3 1.0 CA A:ASP216 4.7 38.6 1.0 CA A:ASN215 4.8 43.7 1.0 CB A:ARG181 4.8 36.5 1.0 CB A:ILE214 4.8 39.9 1.0 CG A:GLU119 4.9 38.2 1.0 N A:ALA249 4.9 40.4 1.0 N A:ASN217 5.0 41.1 1.0 C A:ASN215 5.0 42.1 1.0 CG A:ARG181 5.0 32.6 1.0

Calcium binding site 6 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:35.7 occ:1.00 O A:ASN217 2.4 42.7 1.0 OD1 A:ASN215 2.5 49.5 1.0 OD1 A:ASP248 2.6 46.1 1.0 OD2 A:ASP246 2.7 39.0 1.0 OD1 A:ASN304 2.7 50.6 1.0 O A:ALA254 2.8 38.9 1.0 CG A:ASN304 3.0 47.2 1.0 OD1 A:ASP246 3.0 40.3 1.0 CG A:ASP246 3.2 39.9 1.0 ND2 A:ASN304 3.4 43.1 1.0 CG A:ASN215 3.5 52.4 1.0 C A:ASN217 3.6 46.6 1.0 CB A:ASN304 3.6 47.7 1.0 C A:ALA254 3.7 38.6 1.0 CG A:ASP248 3.8 49.8 1.0 ND2 A:ASN215 4.1 51.4 1.0 CD A:PRO219 4.2 48.2 1.0 CG A:PRO219 4.3 45.1 1.0 CA A:ALA218 4.4 40.6 1.0 N A:TRP255 4.4 36.5 1.0 N A:ALA218 4.4 45.1 1.0 CA A:TRP255 4.4 39.3 1.0 CB A:ASP248 4.4 41.5 1.0 N A:PRO219 4.4 43.7 1.0 CA A:ALA254 4.5 43.0 1.0 C A:ALA218 4.6 43.6 1.0 CA A:ASN217 4.6 40.1 1.0 CB A:ASP246 4.6 41.5 1.0 CB A:ASN215 4.6 46.5 1.0 N A:ASN217 4.7 41.1 1.0 CE1 A:PHE308 4.7 59.6 1.0 CA A:ASN215 4.8 43.7 1.0 OD2 A:ASP248 4.8 44.4 1.0 C A:ASN215 4.9 42.1 1.0 CA A:ASN304 4.9 45.7 1.0

Calcium binding site 7 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 Mouse E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:72.2 occ:1.00 O A:VAL326 2.4 78.5 1.0 OD1 A:ASP325 2.5 67.2 1.0 OE2 A:GLU328 2.6 76.6 1.0 OE1 A:GLU291 2.8 64.0 1.0 OD1 A:ASP360 2.9 88.5 1.0 OE2 A:GLU291 3.0 64.4 1.0 CD A:GLU328 3.1 81.1 1.0 CD A:GLU291 3.1 65.5 1.0 OE1 A:GLU232 3.5 74.9 1.0 CG A:GLU328 3.5 75.5 1.0 C A:VAL326 3.5 79.5 1.0 CG A:ASP325 3.6 64.8 1.0 N A:VAL326 3.8 70.3 1.0 OE1 A:GLU328 3.8 80.1 1.0 CG A:ASP360 4.0 88.6 1.0 N A:GLU328 4.1 82.9 1.0 CA A:ASP360 4.1 80.0 1.0 CB A:GLU328 4.1 76.7 1.0 OD2 A:ASP325 4.1 59.2 1.0 CA A:CA608 4.2 58.4 1.0 CA A:VAL326 4.3 73.5 1.0 CB A:ASP360 4.3 90.2 1.0 CD A:GLU232 4.3 79.3 1.0 OE2 A:GLU232 4.3 83.2 1.0 CG A:GLU291 4.4 67.3 1.0 N A:ASN327 4.5 81.7 1.0 CG1 A:VAL326 4.6 75.1 1.0 C A:ASP325 4.6 68.8 1.0 CA A:ASN327 4.6 83.8 1.0 C A:ASN327 4.7 82.1 1.0 CA A:ASP325 4.7 71.6 1.0 N A:ASP360 4.7 75.0 1.0 CB A:ASP325 4.8 68.8 1.0 CA A:GLU328 4.8 84.3 1.0 O A:PRO359 4.8 64.6 1.0

Calcium binding site 8 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 Mouse E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:58.4 occ:1.00 OE2 A:GLU291 2.5 64.4 1.0 OE2 A:GLU328 2.6 76.6 1.0 OE2 A:GLU232 2.8 83.2 1.0 OE1 A:GLU328 2.9 80.1 1.0 OD1 A:ASP289 3.0 83.5 1.0 OD2 A:ASP289 3.1 66.4 1.0 CD A:GLU328 3.1 81.1 1.0 CD A:GLU291 3.3 65.5 1.0 CG A:ASP289 3.4 74.9 1.0 CB A:GLU291 3.4 60.5 1.0 CG A:GLU291 3.6 67.3 1.0 CD A:GLU232 3.9 79.3 1.0 N A:GLU291 4.0 66.6 1.0 CA A:CA607 4.2 72.2 1.0 OE1 A:GLU232 4.3 74.9 1.0 CA A:GLU291 4.4 61.3 1.0 OE1 A:GLU291 4.4 64.0 1.0 O A:PRO359 4.5 64.6 1.0 N A:PHE290 4.6 68.0 1.0 CG A:GLU328 4.7 75.5 1.0 CB A:ASP289 4.8 68.9 1.0

Calcium binding site 9 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 Mouse E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:87.7 occ:1.00 OD2 A:ASP360 2.5 79.9 1.0 OE1 A:GLN365 2.6 80.5 1.0 OE2 A:GLU358 2.7 83.1 1.0 O A:GLU328 2.7 91.3 1.0 OD2 A:ASP415 2.8 79.3 1.0 ND2 A:ASN327 3.0 87.9 1.0 OD1 A:ASN327 3.3 86.0 1.0 CG A:ASP415 3.3 80.1 1.0 CG A:ASN327 3.4 88.5 1.0 CD A:PRO330 3.4 79.6 1.0 CB A:ALA421 3.4 88.5 1.0 CD A:GLU358 3.5 86.8 1.0 OE1 A:GLU358 3.6 89.6 1.0 C A:GLU328 3.6 94.2 1.0 CD A:GLN365 3.6 87.3 1.0 OD1 A:ASP415 3.7 88.7 1.0 CG A:ASP360 3.8 88.6 1.0 CG A:PRO330 3.8 77.0 1.0 NE2 A:GLN365 4.2 85.9 1.0 N A:GLU328 4.2 82.9 1.0 CA A:ALA329 4.2 79.2 1.0 N A:ALA329 4.3 90.0 1.0 CB A:ASP415 4.3 83.0 1.0 N A:PRO330 4.3 83.2 1.0 O A:ALA421 4.4 86.5 1.0 OD1 A:ASP360 4.5 88.5 1.0 CD A:PRO359 4.5 85.4 1.0 CA A:GLU328 4.6 84.3 1.0 C A:ALA329 4.6 86.7 1.0 CA A:ALA421 4.6 83.8 1.0 C A:ASN327 4.6 82.1 1.0 CB A:ASN327 4.7 86.2 1.0 CB A:ASP360 4.8 90.2 1.0 C A:ALA421 4.8 83.1 1.0 N A:ALA421 4.9 81.8 1.0 CG A:GLN365 4.9 95.1 1.0 CG A:GLU358 4.9 86.2 1.0 CA A:ASN327 4.9 83.8 1.0

Calcium binding site 10 out of 24 in the Crystal Structure of Mouse E-Cadherin Ectodomain


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 Mouse E-Cadherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:74.3 occ:1.00 OD1 A:ASP395 2.5 83.8 1.0 OD1 A:ASP436 2.7 90.2 1.0 OE1 A:GLU343 2.7 80.3 1.0 OE2 A:GLU397 2.9 86.0 1.0 CA A:CA611 2.9 81.1 1.0 OD1 A:ASN437 3.0 90.2 1.0 OD2 A:ASP436 3.2 90.5 1.0 CG A:ASP395 3.3 93.1 1.0 CG A:ASP436 3.3 95.2 1.0 OD2 A:ASP395 3.4 91.1 1.0 CB A:GLU397 3.5 92.4 1.0 CD A:GLU397 3.5 93.6 1.0 CD A:GLU343 3.6 93.3 1.0 CG A:ASN437 3.8 85.3 1.0 ND2 A:ASN437 3.8 76.2 1.0 N A:GLU397 3.8 93.9 1.0 OE2 A:GLU343 3.8 89.6 1.0 CG A:GLU397 4.1 96.7 1.0 OE1 A:GLU397 4.2 99.6 1.0 CA A:GLU397 4.2 93.2 1.0 N A:ARG396 4.5 86.6 1.0 OD1 A:ASP464 4.5 83.6 1.0 CB A:ASP395 4.7 92.6 1.0 C A:GLU397 4.8 88.0 1.0 CB A:ASP436 4.8 0.4 1.0 C A:ARG396 4.9 89.4 1.0 O A:VAL434 4.9 88.0 1.0 CG A:GLU343 4.9 93.6 1.0 CA A:ASP395 5.0 86.7 1.0 C A:ASP395 5.0 86.7 1.0

O.J.Harrison, X.Jin, S.Hong, F.Bahna, G.Ahlsen, J.Brasch, Y.Wu, J.Vendome, K.Felsovalyi, C.M.Hampton, R.B.Troyanovsky, A.Ben-Shaul, J.Frank, S.M.Troyanovsky, L.Shapiro, B.Honig. The Extracellular Architecture of Adherens Junctions Revealed By Crystal Structures of Type I Cadherins. Structure V. 19 244 2011.
ISSN: ISSN 0969-2126
PubMed: 21300292
DOI: 10.1016/J.STR.2010.11.016