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

The structure of Crystal Structure of Human P-Cadherin (Ss-Dimer), PDB code: 4zml 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)	40.46 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	118.950, 80.910, 49.180, 90.00, 105.75, 90.00
R / Rfree (%)	19.5 / 21.8

The structure of Crystal Structure of Human P-Cadherin (Ss-Dimer) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:30.5 occ:1.00 OD2 A:ASP103 2.2 32.7 1.0 OD1 A:ASP100 2.2 38.8 1.0 OE2 A:GLU69 2.3 30.3 1.0 OE2 A:GLU11 2.3 29.1 1.0 O A:GLN101 2.3 34.3 1.0 OD1 A:ASP136 2.3 28.4 1.0 CD A:GLU69 3.0 26.5 1.0 OE1 A:GLU69 3.0 30.9 1.0 CG A:ASP100 3.3 36.1 1.0 CG A:ASP103 3.3 33.0 1.0 CD A:GLU11 3.4 29.5 1.0 CG A:ASP136 3.5 37.2 1.0 C A:GLN101 3.5 35.3 1.0 N A:GLN101 3.8 32.8 1.0 OD2 A:ASP100 3.8 32.2 1.0 OE1 A:GLU11 3.9 26.1 1.0 N A:ASP103 3.9 34.7 1.0 OD1 A:ASP103 3.9 34.3 1.0 CA A:CA302 4.1 32.4 1.0 CD2 A:HIS104 4.1 34.7 1.0 CB A:ASP136 4.3 35.5 1.0 CA A:GLN101 4.3 34.6 1.0 OD2 A:ASP136 4.3 28.7 1.0 CG A:GLU69 4.4 29.3 1.0 CA A:ASP136 4.4 35.9 1.0 NE A:ARG68 4.4 39.8 1.0 CB A:ASP103 4.4 35.9 1.0 CB A:ASP100 4.5 34.5 1.0 NH2 A:ARG68 4.5 40.2 1.0 N A:ASN102 4.6 36.9 1.0 CA A:ASP100 4.6 31.9 1.0 CG A:GLU11 4.6 26.9 1.0 CA A:ASP103 4.6 36.1 1.0 C A:ASP100 4.7 37.9 1.0 CA A:ASN102 4.7 34.8 1.0 C A:ASN102 4.8 36.8 1.0 NE2 A:HIS104 4.9 36.3 1.0 N A:HIS104 5.0 37.2 1.0 CB A:GLN101 5.0 37.3 1.0 CB A:ARG68 5.0 27.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Human P-Cadherin (Ss-Dimer)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:32.4 occ:1.00 OE1 A:GLU69 2.2 30.9 1.0 O A:HOH529 2.3 31.5 1.0 OD1 A:ASP103 2.3 34.3 1.0 O A:HOH417 2.3 30.8 1.0 OE1 A:GLU11 2.4 26.1 1.0 OD1 A:ASP67 2.4 28.4 1.0 CG A:ASP103 3.1 33.0 1.0 OD2 A:ASP103 3.2 32.7 1.0 CD A:GLU11 3.3 29.5 1.0 CG A:ASP67 3.3 30.3 1.0 CD A:GLU69 3.5 26.5 1.0 OE2 A:GLU11 3.7 29.1 1.0 OD2 A:ASP67 4.0 30.2 1.0 CA A:CA301 4.1 30.5 1.0 NE2 A:HIS104 4.2 36.3 1.0 CA A:ASP67 4.2 27.4 1.0 O A:HOH434 4.2 44.2 1.0 OE2 A:GLU69 4.2 30.3 1.0 N A:ARG68 4.2 25.9 1.0 CB A:ASP67 4.2 28.3 1.0 OD1 A:ASN12 4.3 34.7 1.0 N A:GLU69 4.3 27.4 1.0 ND2 A:ASN12 4.4 33.9 1.0 C A:ASP67 4.5 25.7 1.0 CB A:GLU69 4.5 29.4 1.0 CB A:ASP103 4.5 35.9 1.0 CG A:GLU69 4.5 29.3 1.0 O A:HOH542 4.5 47.7 1.0 CG A:GLU11 4.5 26.9 1.0 CD2 A:HIS104 4.6 34.7 1.0 CG A:ASN12 4.7 34.6 1.0 CB A:GLU11 4.9 26.2 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Human P-Cadherin (Ss-Dimer)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:35.2 occ:1.00 O A:HIS104 2.2 38.6 1.0 O A:ASN143 2.3 34.8 1.0 OD1 A:ASN102 2.4 38.8 1.0 OD2 A:ASP136 2.4 28.7 1.0 OD2 A:ASP195 2.4 41.8 1.0 OD1 A:ASP134 2.5 34.2 1.0 OD2 A:ASP134 2.5 34.5 1.0 CG A:ASP134 2.9 36.5 1.0 CG A:ASP195 3.4 43.0 1.0 CG A:ASP136 3.4 37.2 1.0 C A:HIS104 3.4 38.9 1.0 C A:ASN143 3.4 32.1 1.0 CG A:ASN102 3.5 38.7 1.0 CB A:ASP195 3.6 39.9 1.0 CB A:ASP136 3.6 35.5 1.0 ND2 A:ASN102 4.0 38.9 1.0 O A:HOH429 4.2 49.2 1.0 N A:HIS104 4.2 37.2 1.0 CA A:HIS104 4.2 38.9 1.0 N A:GLY144 4.3 32.8 1.0 CB A:ASP134 4.4 32.6 1.0 CA A:ASN143 4.4 35.3 1.0 CB A:HIS104 4.4 37.3 1.0 CA A:GLY144 4.4 34.2 1.0 N A:LYS105 4.5 42.9 1.0 OD1 A:ASP195 4.5 45.4 1.0 OD1 A:ASP136 4.5 28.4 1.0 CA A:LYS105 4.7 42.8 1.0 CB A:ASN102 4.7 38.7 1.0 CB A:ASN143 4.7 37.2 1.0 CA A:ASN102 4.8 34.8 1.0 C A:LYS105 4.8 38.9 1.0 N A:ASP136 4.8 35.0 1.0 CA A:ASP136 4.9 35.9 1.0 C A:ASN102 4.9 36.8 1.0 N A:ASP103 5.0 34.7 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Human P-Cadherin (Ss-Dimer)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:38.1 occ:0.50 O A:HOH539 2.4 40.7 1.0 O A:HOH531 2.4 34.3 1.0 OE2 A:GLU70 2.5 36.3 1.0 OE1 A:GLU70 2.6 37.2 1.0 CD A:GLU70 2.9 40.3 1.0 O A:HOH563 4.2 42.4 1.0 CG A:GLU70 4.4 36.9 1.0 O A:HOH580 4.6 42.5 1.0 O A:HOH454 4.6 30.2 1.0 C11 A:P6G308 4.6 49.4 1.0 O A:HOH450 4.8 39.7 1.0 O A:HOH409 4.9 35.9 1.0 CB A:GLU70 5.0 30.7 1.0 C12 A:P6G308 5.0 49.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Human P-Cadherin (Ss-Dimer)


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 (Ss-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:53.0 occ:1.00 O A:HOH521 2.0 50.1 1.0 OE1 A:GLU182 2.7 64.6 1.0 CD A:GLU182 3.5 64.2 1.0 CG A:GLU182 3.7 59.7 1.0 OD1 A:ASP180 4.1 53.4 1.0 CB A:GLU182 4.2 58.0 1.0 OE2 A:GLU119 4.5 60.3 1.0 OE2 A:GLU182 4.6 70.1 1.0 OE1 A:GLU119 4.7 56.1 1.0 N A:GLU182 4.9 52.8 1.0 OD1 A:ASP213 4.9 81.0 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