Calcium in PDB 4zmz: Crystal Structure of Human P-Cadherin (Monomer 2)

The structure of Crystal Structure of Human P-Cadherin (Monomer 2), PDB code: 4zmz 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)	32.42 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.660, 40.740, 72.860, 90.00, 94.66, 90.00
R / Rfree (%)	21.6 / 26.6

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

Calcium binding site 1 out of 4 in the Crystal Structure of Human P-Cadherin (Monomer 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:30.6 occ:1.00 OD1 A:ASP103 2.4 32.3 1.0 OE2 A:GLU69 2.4 35.9 1.0 OD1 A:ASP100 2.4 30.7 1.0 OD1 A:ASP136 2.4 26.7 1.0 O A:GLN101 2.4 33.0 1.0 OE2 A:GLU11 2.4 34.4 1.0 CD A:GLU69 3.1 36.6 1.0 OE1 A:GLU69 3.1 36.2 1.0 CG A:ASP100 3.5 32.1 1.0 CG A:ASP136 3.5 26.6 1.0 CD A:GLU11 3.5 34.6 1.0 CG A:ASP103 3.5 33.5 1.0 C A:GLN101 3.6 33.1 1.0 OE1 A:GLU11 3.8 35.2 1.0 N A:ASP103 3.9 31.2 1.0 N A:GLN101 4.0 32.4 1.0 OD2 A:ASP100 4.0 33.4 1.0 CD2 A:HIS104 4.0 38.6 1.0 CB A:ASP136 4.1 25.6 1.0 OD2 A:ASP103 4.1 33.5 1.0 CA A:CA303 4.2 35.2 1.0 CA A:ASP136 4.3 26.6 1.0 OD2 A:ASP136 4.4 24.6 1.0 CA A:GLN101 4.4 34.1 1.0 NE A:ARG68 4.5 40.4 1.0 CG A:GLU69 4.5 37.8 1.0 CB A:ASP103 4.6 33.1 1.0 N A:ASN102 4.6 31.4 1.0 CB A:ASP100 4.6 32.0 1.0 CA A:ASN102 4.7 30.1 1.0 CA A:ASP100 4.7 31.5 1.0 CA A:ASP103 4.7 31.8 1.0 NH2 A:ARG68 4.7 43.5 1.0 CG A:GLU11 4.8 34.8 1.0 NE2 A:HIS104 4.8 41.7 1.0 C A:ASN102 4.8 30.7 1.0 C A:ASP100 4.8 32.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin (Monomer 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.1 occ:1.00 OD1 A:ASN102 2.2 30.3 1.0 OD2 A:ASP136 2.3 24.6 1.0 O A:ASN143 2.3 25.3 1.0 OD2 A:ASP195 2.3 23.5 1.0 O A:HIS104 2.4 28.1 1.0 OD2 A:ASP134 2.6 23.3 1.0 OD1 A:ASP134 2.6 25.3 1.0 CG A:ASP134 3.0 24.7 1.0 CG A:ASP195 3.3 25.6 1.0 CG A:ASP136 3.3 26.6 1.0 CG A:ASN102 3.3 28.5 1.0 C A:HIS104 3.5 33.9 1.0 C A:ASN143 3.5 25.7 1.0 CB A:ASP195 3.7 24.4 1.0 CB A:ASP136 3.8 25.6 1.0 ND2 A:ASN102 4.0 27.2 1.0 N A:HIS104 4.1 34.9 1.0 O A:HOH457 4.1 38.0 1.0 CA A:HIS104 4.1 35.0 1.0 CB A:HIS104 4.3 36.5 1.0 N A:GLY144 4.4 23.8 1.0 CA A:GLY144 4.4 24.1 1.0 OD1 A:ASP195 4.4 25.1 1.0 CB A:ASP134 4.4 25.5 1.0 OD1 A:ASP136 4.4 26.7 1.0 CA A:ASN143 4.5 25.2 1.0 CB A:ASN102 4.5 29.7 1.0 N A:LYS105 4.6 31.9 1.0 CA A:ASN102 4.7 30.1 1.0 N A:ASP136 4.8 27.5 1.0 CB A:ASN143 4.8 25.7 1.0 CA A:ASP136 4.9 26.6 1.0 CA A:LYS105 4.9 33.6 1.0 C A:ASN102 4.9 30.7 1.0 C A:LYS105 5.0 32.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin (Monomer 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:35.2 occ:1.00 OD2 A:ASP103 2.2 33.5 1.0 OD1 A:ASP67 2.3 36.8 1.0 O A:HOH415 2.4 27.8 1.0 OE1 A:GLU69 2.4 36.2 1.0 OE1 A:GLU11 2.6 35.2 1.0 CG A:ASP103 3.1 33.5 1.0 OD1 A:ASP103 3.3 32.3 1.0 CG A:ASP67 3.3 37.1 1.0 CD A:GLU11 3.4 34.6 1.0 CD A:GLU69 3.7 36.6 1.0 OE2 A:GLU11 3.8 34.4 1.0 OD2 A:ASP67 4.1 36.5 1.0 N A:ARG68 4.1 34.8 1.0 CA A:ASP67 4.1 35.7 1.0 CB A:ASP67 4.1 35.9 1.0 CA A:CA301 4.2 30.6 1.0 NE2 A:HIS104 4.2 41.7 1.0 OD1 A:ASN12 4.3 33.4 1.0 OE2 A:GLU69 4.3 35.9 1.0 ND2 A:ASN12 4.4 35.8 1.0 C A:ASP67 4.5 35.4 1.0 O A:HOH446 4.5 39.8 1.0 N A:GLU69 4.5 37.6 1.0 CB A:ASP103 4.5 33.1 1.0 CD2 A:HIS104 4.5 38.6 1.0 O A:HOH431 4.6 34.0 1.0 CG A:GLU11 4.6 34.8 1.0 CB A:GLU69 4.7 38.5 1.0 CG A:GLU69 4.7 37.8 1.0 CG A:ASN12 4.8 36.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin (Monomer 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:50.0 occ:1.00 O A:HOH401 2.2 27.4 1.0 O A:ASP199 2.6 23.6 1.0 O A:GLY200 2.9 25.1 1.0 C A:ASP199 3.6 24.0 1.0 C A:GLY200 3.6 25.0 1.0 CA A:GLY200 3.8 24.1 1.0 N A:GLY200 4.1 23.9 1.0 N A:SER201 4.6 27.5 1.0 CA A:ASP199 4.7 25.1 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