Calcium in PDB 4zmy: Crystal Structure of Human P-Cadherin (Monomer 1)

The structure of Crystal Structure of Human P-Cadherin (Monomer 1), PDB code: 4zmy was solved by J.M.M.Caaveiro, S.Kudo, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.22 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.840, 40.910, 72.480, 90.00, 97.27, 90.00
R / Rfree (%)	13.7 / 18.6

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Monomer 1) (pdb code 4zmy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Monomer 1), PDB code: 4zmy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.6 occ:1.00 OD1 A:ASP136 2.3 16.3 1.0 OD1 A:ASP100 2.3 17.5 1.0 OD1 A:ASP103 2.4 17.1 1.0 OE2 A:GLU11 2.4 16.1 1.0 O A:GLN101 2.4 17.4 1.0 OE2 A:GLU69 2.4 17.7 1.0 OE1 A:GLU69 3.1 18.8 1.0 CD A:GLU69 3.1 18.0 1.0 CG A:ASP100 3.3 14.6 1.0 CG A:ASP136 3.4 16.0 1.0 CG A:ASP103 3.4 20.8 1.0 CD A:GLU11 3.5 16.6 1.0 C A:GLN101 3.6 16.0 1.0 OD2 A:ASP100 3.8 18.1 1.0 OE1 A:GLU11 3.9 17.9 1.0 N A:GLN101 3.9 16.0 1.0 N A:ASP103 3.9 16.2 1.0 OD2 A:ASP103 4.0 19.9 1.0 CA A:CA303 4.1 19.6 1.0 CB A:ASP136 4.2 14.1 1.0 CD2 A:HIS104 4.2 19.2 1.0 OD2 A:ASP136 4.3 15.3 1.0 CA A:GLN101 4.4 16.8 1.0 CA A:ASP136 4.4 14.5 1.0 NE A:ARG68 4.5 23.8 1.0 CB A:ASP103 4.5 18.3 1.0 CG A:GLU69 4.5 18.9 1.0 CB A:ASP100 4.6 16.2 1.0 N A:ASN102 4.6 16.9 1.0 NH2 A:ARG68 4.6 21.1 1.0 CA A:ASP103 4.7 18.2 1.0 CA A:ASP100 4.7 16.4 1.0 CA A:ASN102 4.7 17.8 1.0 CG A:GLU11 4.7 17.4 1.0 C A:ASP100 4.8 15.1 1.0 C A:ASN102 4.8 17.2 1.0 N A:HIS104 5.0 16.7 1.0 NE2 A:HIS104 5.0 24.8 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:15.0 occ:1.00 O A:HIS104 2.2 15.5 1.0 OD1 A:ASN102 2.3 17.9 1.0 OD2 A:ASP195 2.3 15.3 1.0 OD2 A:ASP136 2.4 15.3 1.0 O A:ASN143 2.4 15.2 1.0 OD2 A:ASP134 2.4 15.0 1.0 OD1 A:ASP134 2.5 13.0 1.0 CG A:ASP134 2.8 12.0 1.0 CG A:ASP195 3.3 13.3 1.0 CG A:ASP136 3.4 16.0 1.0 C A:HIS104 3.5 14.2 1.0 CG A:ASN102 3.5 16.8 1.0 C A:ASN143 3.6 16.1 1.0 CB A:ASP195 3.6 13.1 1.0 CB A:ASP136 3.7 14.1 1.0 ND2 A:ASN102 4.1 16.8 1.0 N A:HIS104 4.1 16.7 1.0 CA A:HIS104 4.2 16.5 1.0 O A:HOH449 4.3 22.2 1.0 CB A:ASP134 4.3 13.2 1.0 OD1 A:ASP195 4.4 15.2 1.0 N A:GLY144 4.4 15.2 1.0 CA A:GLY144 4.5 14.1 1.0 CB A:HIS104 4.5 17.6 1.0 N A:LYS105 4.5 16.4 1.0 CA A:ASN143 4.5 15.2 1.0 OD1 A:ASP136 4.5 16.3 1.0 CB A:ASN102 4.7 18.3 1.0 CA A:ASN102 4.8 17.8 1.0 CA A:LYS105 4.8 14.8 1.0 N A:ASP136 4.8 14.5 1.0 CB A:ASN143 4.8 16.4 1.0 N A:ASP103 4.8 16.2 1.0 C A:LYS105 4.9 13.8 1.0 CA A:ASP136 4.9 14.5 1.0 C A:ASN102 4.9 17.2 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:19.6 occ:1.00 O A:HOH594 2.2 22.1 1.0 OD2 A:ASP103 2.3 19.9 1.0 OD1 A:ASP67 2.3 20.3 1.0 OE1 A:GLU69 2.3 18.8 1.0 OE1 A:GLU11 2.4 17.9 1.0 O A:HOH441 2.4 18.5 1.0 CG A:ASP103 3.0 20.8 1.0 OD1 A:ASP103 3.1 17.1 1.0 CG A:ASP67 3.2 23.2 1.0 CD A:GLU11 3.3 16.6 1.0 CD A:GLU69 3.5 18.0 1.0 OE2 A:GLU11 3.6 16.1 1.0 OD2 A:ASP67 4.0 23.0 1.0 CA A:CA301 4.1 16.6 1.0 N A:ARG68 4.1 18.7 1.0 CB A:ASP67 4.1 20.6 1.0 CA A:ASP67 4.1 20.0 1.0 O A:HOH535 4.1 29.6 1.0 NE2 A:HIS104 4.1 24.8 1.0 OE2 A:GLU69 4.3 17.7 1.0 N A:GLU69 4.3 18.9 1.0 OD1 A:ASN12 4.4 20.7 1.0 C A:ASP67 4.4 17.6 1.0 ND2 A:ASN12 4.4 17.8 1.0 O A:HOH598 4.4 37.3 1.0 CB A:ASP103 4.5 18.3 1.0 CD2 A:HIS104 4.5 19.2 1.0 CB A:GLU69 4.5 19.6 1.0 CG A:GLU69 4.6 18.9 1.0 CG A:GLU11 4.6 17.4 1.0 O A:HOH480 4.7 25.5 1.0 CG A:ASN12 4.8 19.4 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:29.9 occ:0.75 O A:HOH662 2.0 42.1 1.0 CA A:CA307 2.3 29.5 0.8 O A:HOH409 2.4 35.2 1.0 OE2 A:GLU119 2.4 24.2 1.0 O A:HOH621 2.4 31.2 1.0 CD A:GLU119 3.6 24.6 1.0 O A:HOH684 4.3 34.3 1.0 CG A:GLU119 4.3 21.3 1.0 O A:HOH676 4.4 34.9 1.0 OE1 A:GLU119 4.5 24.7 1.0 O A:HOH481 4.6 34.0 1.0 O A:HOH514 4.9 42.3 1.0 CB A:GLU119 5.0 17.9 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:27.2 occ:0.75 O A:GLU69 2.3 27.1 1.0 O A:HOH611 2.4 48.1 0.8 O A:HOH540 2.5 39.4 1.0 O A:HOH630 2.6 44.0 0.8 O A:HOH500 2.9 40.2 1.0 C A:GLU69 3.5 21.2 1.0 CA A:GLU70 4.3 24.5 1.0 N A:GLU70 4.3 19.7 1.0 CA A:GLU69 4.5 20.1 1.0 O A:GLU70 4.5 20.4 1.0 O A:HOH486 4.6 36.5 1.0 CB A:GLU69 4.6 19.6 1.0 C A:GLU70 4.8 20.4 1.0 O A:HOH433 4.9 33.9 1.0 OE1 A:GLU135 5.0 32.2 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:29.7 occ:0.75 O A:HOH607 2.3 37.2 1.0 O A:HOH462 2.3 36.5 1.0 OXT A:ASP213 2.4 34.4 1.0 O A:HOH595 2.4 37.1 1.0 O A:HOH635 2.4 26.0 0.5 O A:HOH678 2.5 27.2 0.8 C A:ASP213 3.5 27.8 1.0 CA A:ASP213 4.0 26.7 1.0 CB A:ASP213 4.0 33.0 1.0 O A:HOH616 4.1 28.7 0.5 O A:ASP213 4.5 24.6 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Human P-Cadherin (Monomer 1)


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 P-Cadherin (Monomer 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca307 b:29.5 occ:0.75 O A:HOH621 2.0 31.2 1.0 CA A:CA304 2.3 29.9 0.8 O A:HOH676 2.4 34.9 1.0 O A:HOH662 2.5 42.1 1.0 O A:HOH684 2.7 34.3 1.0 O A:HOH481 4.3 34.0 1.0 OE2 A:GLU119 4.4 24.2 1.0 O A:HOH409 4.6 35.2 1.0 CA A:GLY120 4.8 14.1 1.0 O A:HOH559 5.0 25.8 1.0

S.Kudo, J.M.Caaveiro, K.Tsumoto. Adhesive Dimerization of Human P-Cadherin Catalyzed By A Chaperone-Like Mechanism Structure V. 24 1523 2016.
ISSN: ISSN 0969-2126
PubMed: 27545624
DOI: 10.1016/J.STR.2016.07.002