Calcium in PDB 4zmp: Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L)

The structure of Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L), PDB code: 4zmp 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)	35.74 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.700, 77.990, 49.230, 90.00, 105.78, 90.00
R / Rfree (%)	22.2 / 25.2

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L) (pdb code 4zmp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L), PDB code: 4zmp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L)


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 Q101L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:44.5 occ:1.00 OD2 A:ASP103 2.0 37.1 1.0 OE2 A:GLU69 2.2 35.8 1.0 O A:LEU101 2.2 43.3 1.0 OD1 A:ASP100 2.3 46.8 1.0 OE2 A:GLU11 2.3 47.2 1.0 OD1 A:ASP136 2.4 44.2 1.0 OE1 A:GLU69 2.8 42.7 1.0 CD A:GLU69 2.9 38.7 1.0 CG A:ASP103 3.2 42.3 1.0 CG A:ASP100 3.2 45.9 1.0 CD A:GLU11 3.5 47.1 1.0 C A:LEU101 3.5 46.5 1.0 CG A:ASP136 3.5 43.5 1.0 OD2 A:ASP100 3.7 46.4 1.0 N A:LEU101 3.8 44.2 1.0 OD1 A:ASP103 3.9 46.4 1.0 N A:ASP103 3.9 50.6 1.0 OE1 A:GLU11 3.9 46.9 1.0 CA A:CA302 4.0 48.5 1.0 CB A:ASP136 4.2 43.8 1.0 CD2 A:HIS104 4.3 52.4 1.0 CG A:GLU69 4.3 41.9 1.0 CA A:LEU101 4.3 46.0 1.0 NH2 A:ARG68 4.3 49.2 1.0 CB A:ASP103 4.3 43.4 1.0 NE A:ARG68 4.3 48.9 1.0 CA A:ASP136 4.4 45.6 1.0 OD2 A:ASP136 4.4 46.6 1.0 N A:ASN102 4.5 45.9 1.0 CB A:ASP100 4.5 45.9 1.0 CA A:ASP103 4.6 49.6 1.0 CA A:ASP100 4.6 45.2 1.0 C A:ASP100 4.7 44.0 1.0 CA A:ASN102 4.7 48.8 1.0 CG A:GLU11 4.7 43.2 1.0 C A:ASN102 4.8 50.6 1.0 CZ A:ARG68 4.8 50.2 1.0 N A:HIS104 4.9 54.6 1.0 CB A:LEU101 5.0 46.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L)


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 Q101L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:48.5 occ:1.00 OD1 A:ASP103 2.0 46.4 1.0 OD1 A:ASP67 2.1 38.9 1.0 OE1 A:GLU69 2.2 42.7 1.0 O A:HOH428 2.3 40.3 1.0 O A:HOH407 2.3 41.9 1.0 OE1 A:GLU11 2.4 46.9 1.0 CG A:ASP103 3.0 42.3 1.0 CG A:ASP67 3.1 42.0 1.0 OD2 A:ASP103 3.2 37.1 1.0 CD A:GLU11 3.3 47.1 1.0 CD A:GLU69 3.4 38.7 1.0 OE2 A:GLU11 3.6 47.2 1.0 OD2 A:ASP67 3.8 40.3 1.0 CA A:CA301 4.0 44.5 1.0 N A:ARG68 4.0 38.8 1.0 OD1 A:ASN12 4.1 45.0 1.0 CB A:ASP67 4.2 41.6 1.0 OE2 A:GLU69 4.2 35.8 1.0 CA A:ASP67 4.2 41.9 1.0 NE2 A:HIS104 4.2 54.2 1.0 N A:GLU69 4.3 41.8 1.0 CB A:GLU69 4.3 42.6 1.0 CB A:ASP103 4.3 43.4 1.0 CG A:GLU69 4.4 41.9 1.0 ND2 A:ASN12 4.4 50.0 1.0 C A:ASP67 4.5 44.5 1.0 CD2 A:HIS104 4.6 52.4 1.0 CG A:GLU11 4.6 43.2 1.0 CG A:ASN12 4.7 49.7 1.0 CA A:GLU69 4.9 45.0 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human P-Cadherin (Ss-Dimer Q101L)


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 Q101L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:54.1 occ:1.00 OD2 A:ASP195 2.2 55.1 1.0 O A:HIS104 2.2 54.1 1.0 O A:ASN143 2.3 39.9 1.0 OD1 A:ASN102 2.4 54.3 1.0 OD2 A:ASP136 2.4 46.6 1.0 OD2 A:ASP134 2.4 50.2 1.0 OD1 A:ASP134 2.7 54.6 1.0 CG A:ASP134 2.9 54.3 1.0 CG A:ASP195 3.1 52.6 1.0 C A:HIS104 3.4 53.9 1.0 CG A:ASP136 3.4 43.5 1.0 CB A:ASP195 3.5 50.2 1.0 C A:ASN143 3.5 42.6 1.0 CG A:ASN102 3.5 53.7 1.0 CB A:ASP136 3.8 43.8 1.0 CA A:HIS104 4.2 53.1 1.0 ND2 A:ASN102 4.2 55.2 1.0 N A:HIS104 4.2 54.6 1.0 OD1 A:ASP195 4.3 54.5 1.0 CB A:HIS104 4.3 53.2 1.0 CA A:ASN143 4.4 47.8 1.0 N A:LYS105 4.4 55.2 1.0 CB A:ASP134 4.4 51.9 1.0 OD1 A:ASP136 4.4 44.2 1.0 N A:GLY144 4.5 40.9 1.0 CA A:LYS105 4.6 59.6 1.0 CB A:ASN102 4.7 49.8 1.0 CA A:ASN102 4.7 48.8 1.0 C A:LYS105 4.7 54.2 1.0 CB A:ASN143 4.7 47.1 1.0 CA A:GLY144 4.8 44.5 1.0 N A:ASP136 4.8 47.8 1.0 C A:ASN102 4.9 50.6 1.0 CA A:ASP136 4.9 45.6 1.0 OG A:SER201 5.0 73.5 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