Calcium in PDB 4zmn: Crystal Structure of Human P-Cadherin (Ss-Dimer Long)

The structure of Crystal Structure of Human P-Cadherin (Ss-Dimer Long), PDB code: 4zmn 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)	35.67 / 2.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.980, 108.980, 93.160, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 24.3

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-Dimer Long) (pdb code 4zmn). 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 (Ss-Dimer Long), PDB code: 4zmn:
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 (Ss-Dimer Long)


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 (Ss-Dimer Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:36.8 occ:1.00 OD2 A:ASP103 2.2 34.8 1.0 O A:HOH401 2.2 32.0 1.0 OE1 A:GLU69 2.2 29.1 1.0 OE1 A:GLU11 2.3 27.6 1.0 OD1 A:ASP67 2.5 29.8 1.0 O A:HOH412 2.5 40.5 1.0 CG A:ASP103 3.1 34.0 1.0 CD A:GLU11 3.2 28.4 1.0 OD1 A:ASP103 3.2 34.0 1.0 CG A:ASP67 3.4 32.9 1.0 CD A:GLU69 3.5 27.8 1.0 OE2 A:GLU11 3.5 27.3 1.0 OD2 A:ASP67 4.0 34.0 1.0 CA A:CA303 4.1 32.2 1.0 OD1 A:ASN12 4.1 29.4 1.0 NE2 A:HIS104 4.2 34.5 1.0 ND2 A:ASN12 4.3 35.5 1.0 CA A:ASP67 4.3 30.4 1.0 OE2 A:GLU69 4.3 24.2 1.0 CB A:ASP67 4.3 29.7 1.0 CB A:GLU69 4.4 28.5 1.0 CG A:GLU69 4.4 26.7 1.0 CG A:GLU11 4.4 27.7 1.0 N A:ARG68 4.4 31.6 1.0 N A:GLU69 4.4 30.0 1.0 CB A:ASP103 4.5 33.2 1.0 CD2 A:HIS104 4.6 33.4 1.0 CG A:ASN12 4.7 31.8 1.0 C A:ASP67 4.7 30.1 1.0 O A:HOH431 4.7 37.0 1.0

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


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 (Ss-Dimer Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:36.2 occ:1.00 O A:HIS104 2.2 37.8 1.0 OD1 A:ASP134 2.3 36.8 1.0 OD1 A:ASN102 2.3 28.8 1.0 O A:ASN143 2.4 31.2 1.0 OD2 A:ASP195 2.5 31.4 1.0 OD2 A:ASP134 2.6 41.3 1.0 OD2 A:ASP136 2.6 38.7 1.0 CG A:ASP134 2.8 35.2 1.0 C A:HIS104 3.4 36.2 1.0 CG A:ASN102 3.4 29.5 1.0 CG A:ASP195 3.4 28.7 1.0 C A:ASN143 3.5 29.2 1.0 CG A:ASP136 3.6 36.4 1.0 CB A:ASP195 3.7 25.6 1.0 CB A:ASP136 3.9 32.8 1.0 ND2 A:ASN102 4.0 28.1 1.0 CA A:HIS104 4.2 32.5 1.0 CB A:ASP134 4.2 35.1 1.0 N A:HIS104 4.3 32.8 1.0 CB A:HIS104 4.3 32.8 1.0 N A:LYS105 4.3 37.4 1.0 CA A:ASN143 4.4 30.8 1.0 CA A:LYS105 4.4 38.8 1.0 N A:GLY144 4.4 28.1 1.0 CA A:GLY144 4.5 25.7 1.0 OD1 A:ASP195 4.5 27.3 1.0 CB A:ASN143 4.5 29.9 1.0 CB A:ASN102 4.7 30.0 1.0 OD1 A:ASP136 4.7 38.5 1.0 CA A:ASN102 4.8 33.1 1.0 C A:LYS105 4.8 36.0 1.0 N A:ASP136 4.9 31.9 1.0 C A:ASN102 4.9 35.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-Dimer Long)


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 (Ss-Dimer Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:32.2 occ:1.00 OD1 A:ASP136 2.2 38.5 1.0 OE2 A:GLU11 2.3 27.3 1.0 OD1 A:ASP103 2.3 34.0 1.0 O A:GLN101 2.3 32.7 1.0 OE2 A:GLU69 2.4 24.2 1.0 OD1 A:ASP100 2.4 25.6 1.0 OE1 A:GLU69 2.9 29.1 1.0 CD A:GLU69 2.9 27.8 1.0 CG A:ASP136 3.2 36.4 1.0 CG A:ASP103 3.4 34.0 1.0 CD A:GLU11 3.4 28.4 1.0 CG A:ASP100 3.4 30.9 1.0 C A:GLN101 3.5 33.1 1.0 N A:GLN101 3.7 33.5 1.0 N A:ASP103 3.9 35.9 1.0 CB A:ASP136 3.9 32.8 1.0 OE1 A:GLU11 3.9 27.6 1.0 OD2 A:ASP100 4.0 35.7 1.0 OD2 A:ASP103 4.0 34.8 1.0 CA A:ASP136 4.1 33.6 1.0 CA A:CA301 4.1 36.8 1.0 OD2 A:ASP136 4.1 38.7 1.0 CD2 A:HIS104 4.2 33.4 1.0 CA A:GLN101 4.2 33.6 1.0 CG A:GLU69 4.3 26.7 1.0 CB A:ASP103 4.4 33.2 1.0 NE A:ARG68 4.5 39.3 1.0 N A:ASN102 4.6 31.1 1.0 CA A:ASP103 4.6 32.4 1.0 CB A:ASP100 4.6 32.0 1.0 C A:ASP100 4.6 30.4 1.0 CB A:GLN101 4.6 36.5 1.0 CA A:ASP100 4.6 30.9 1.0 CG A:GLU11 4.7 27.7 1.0 CA A:ASN102 4.7 33.1 1.0 C A:ASN102 4.8 35.9 1.0 N A:ASP136 4.9 31.9 1.0 NH2 A:ARG68 4.9 38.2 1.0 CB A:ARG68 5.0 31.5 1.0 NE2 A:HIS104 5.0 34.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-Dimer Long)


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 (Ss-Dimer Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:52.6 occ:1.00 O A:HOH427 2.2 34.9 1.0 O A:HOH435 2.5 35.4 1.0 OD2 A:ASP199 2.7 37.5 1.0 CG A:ASP199 3.7 37.0 1.0 OD1 A:ASP199 4.0 37.9 1.0 CB A:ASP199 5.0 35.0 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