Calcium in PDB 4zmx: Crystal Structure of Human P-Cadherin (Int-X-Dimer)

The structure of Crystal Structure of Human P-Cadherin (Int-X-Dimer), PDB code: 4zmx 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)	43.59 / 3.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	181.460, 181.460, 40.730, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.5

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

Calcium binding site 1 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:56.1 occ:1.00 OD1 A:ASP67 2.2 59.3 1.0 OD2 A:ASP103 2.3 52.8 1.0 OE1 A:GLU69 2.3 58.1 1.0 OE1 A:GLU11 2.3 49.7 1.0 CG A:ASP67 3.1 60.2 1.0 CG A:ASP103 3.3 50.9 1.0 CD A:GLU11 3.3 48.5 1.0 CD A:GLU69 3.5 56.1 1.0 OD1 A:ASP103 3.5 50.6 1.0 OD2 A:ASP67 3.6 60.7 1.0 OE2 A:GLU11 3.7 47.0 1.0 OD1 A:ASN12 4.0 48.3 1.0 OE2 A:GLU69 4.1 53.8 1.0 ND2 A:ASN12 4.1 51.9 1.0 CA A:ASP67 4.1 60.4 1.0 CB A:ASP67 4.2 61.8 1.0 CA A:CA302 4.2 45.8 1.0 N A:ARG68 4.3 59.0 1.0 NE2 A:HIS104 4.4 52.6 1.0 C A:ASP67 4.4 60.2 1.0 N A:GLU69 4.4 59.4 1.0 CG A:GLU69 4.5 56.4 1.0 CG A:ASN12 4.5 50.2 1.0 CB A:GLU69 4.5 58.5 1.0 CG A:GLU11 4.6 49.1 1.0 CB A:ASP103 4.6 49.8 1.0 CD2 A:HIS104 4.8 50.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:45.8 occ:1.00 OE2 A:GLU69 2.3 53.8 1.0 OD1 A:ASP100 2.3 44.0 1.0 OD1 A:ASP136 2.4 47.4 1.0 OE2 A:GLU11 2.4 47.0 1.0 O A:GLN101 2.4 42.6 1.0 OD1 A:ASP103 2.4 50.6 1.0 CD A:GLU69 3.2 56.1 1.0 CG A:ASP100 3.2 42.8 1.0 OE1 A:GLU69 3.3 58.1 1.0 CG A:ASP136 3.5 45.8 1.0 CG A:ASP103 3.5 50.9 1.0 CD A:GLU11 3.5 48.5 1.0 OD2 A:ASP100 3.5 40.9 1.0 C A:GLN101 3.6 43.0 1.0 N A:GLN101 3.8 44.6 1.0 OE1 A:GLU11 4.0 49.7 1.0 OD2 A:ASP103 4.0 52.8 1.0 N A:ASP103 4.1 45.9 1.0 CB A:ASP136 4.1 45.1 1.0 CD2 A:HIS104 4.2 50.3 1.0 CA A:CA301 4.2 56.1 1.0 CA A:ASP136 4.3 45.9 1.0 CA A:GLN101 4.3 44.0 1.0 NE A:ARG68 4.3 55.3 1.0 OD2 A:ASP136 4.4 44.8 1.0 CB A:ASP100 4.5 43.9 1.0 CG A:GLU69 4.6 56.4 1.0 CB A:ASP103 4.6 49.8 1.0 N A:ASN102 4.6 42.6 1.0 NH2 A:ARG68 4.7 54.4 1.0 CG A:GLU11 4.7 49.1 1.0 CA A:ASP100 4.7 45.3 1.0 CA A:ASP103 4.8 47.5 1.0 C A:ASP100 4.8 44.5 1.0 CA A:ASN102 4.8 42.5 1.0 NE2 A:HIS104 4.9 52.6 1.0 CB A:GLN101 4.9 44.9 1.0 C A:ASN102 5.0 43.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:30.6 occ:1.00 O A:HIS104 2.3 42.7 1.0 OD1 A:ASN102 2.3 40.2 1.0 OD2 A:ASP136 2.3 44.8 1.0 O A:ASN143 2.4 36.9 1.0 OD2 A:ASP134 2.4 38.9 1.0 OD2 A:ASP195 2.5 37.4 1.0 OD1 A:ASP134 2.6 40.6 1.0 CG A:ASP134 2.9 39.5 1.0 CG A:ASP136 3.4 45.8 1.0 C A:HIS104 3.5 43.9 1.0 CG A:ASN102 3.5 40.4 1.0 CG A:ASP195 3.5 36.4 1.0 C A:ASN143 3.5 37.2 1.0 CB A:ASP195 3.7 35.3 1.0 CB A:ASP136 3.8 45.1 1.0 ND2 A:ASN102 4.1 40.2 1.0 N A:HIS104 4.2 46.1 1.0 CA A:HIS104 4.2 45.8 1.0 CA A:ASN143 4.3 37.5 1.0 CB A:ASP134 4.4 39.1 1.0 CB A:HIS104 4.4 46.3 1.0 N A:LYS105 4.5 44.1 1.0 OD1 A:ASP136 4.5 47.4 1.0 N A:GLY144 4.5 37.3 1.0 CB A:ASN143 4.6 38.7 1.0 CA A:LYS105 4.6 43.4 1.0 OD1 A:ASP195 4.6 36.4 1.0 CB A:ASN102 4.7 41.4 1.0 CA A:GLY144 4.7 36.8 1.0 CA A:ASN102 4.7 42.5 1.0 C A:ASN102 4.8 43.6 1.0 C A:LYS105 4.9 42.0 1.0 N A:ASP136 4.9 45.7 1.0 CD A:PRO106 5.0 39.2 1.0 O A:ASN102 5.0 42.9 1.0 N A:PRO106 5.0 39.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:45.1 occ:1.00 OD1 B:ASP67 2.1 45.8 1.0 OD2 B:ASP103 2.2 43.7 1.0 OE1 B:GLU69 2.4 43.0 1.0 OE1 B:GLU11 2.5 39.3 1.0 CG B:ASP67 3.1 46.2 1.0 CG B:ASP103 3.2 42.8 1.0 CD B:GLU11 3.5 39.0 1.0 OD1 B:ASP103 3.6 42.6 1.0 CD B:GLU69 3.7 42.6 1.0 OD2 B:ASP67 3.8 46.9 1.0 OE2 B:GLU11 3.9 38.0 1.0 CB B:ASP67 4.0 46.1 1.0 ND2 B:ASN12 4.0 39.8 1.0 CA B:ASP67 4.1 44.9 1.0 CE1 B:HIS104 4.2 44.2 1.0 OD1 B:ASN12 4.2 40.9 1.0 CA B:CA302 4.4 41.6 1.0 CB B:GLU69 4.4 44.5 1.0 N B:ARG68 4.5 43.4 1.0 OE2 B:GLU69 4.5 41.5 1.0 N B:GLU69 4.5 44.9 1.0 C B:ASP67 4.5 44.2 1.0 CG B:ASN12 4.5 40.2 1.0 CG B:GLU69 4.6 43.3 1.0 CB B:ASP103 4.6 42.6 1.0 CG B:GLU11 4.8 39.5 1.0 ND1 B:HIS104 4.9 43.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:41.6 occ:1.00 OD1 B:ASP100 2.2 40.8 1.0 OD1 B:ASP103 2.3 42.6 1.0 O B:GLN101 2.3 38.9 1.0 OE2 B:GLU69 2.4 41.5 1.0 OD1 B:ASP136 2.4 40.8 1.0 OE2 B:GLU11 2.4 38.0 1.0 CD B:GLU69 3.1 42.6 1.0 OE1 B:GLU69 3.1 43.0 1.0 CG B:ASP100 3.2 41.3 1.0 CG B:ASP103 3.4 42.8 1.0 CG B:ASP136 3.5 41.3 1.0 C B:GLN101 3.5 39.8 1.0 CD B:GLU11 3.6 39.0 1.0 OD2 B:ASP100 3.7 41.4 1.0 N B:GLN101 3.8 40.4 1.0 OD2 B:ASP103 3.9 43.7 1.0 N B:ASP103 4.0 40.7 1.0 ND1 B:HIS104 4.0 43.2 1.0 OE1 B:GLU11 4.0 39.3 1.0 CB B:ASP136 4.1 41.4 1.0 CA B:ASP136 4.2 42.2 1.0 CA B:GLN101 4.3 40.1 1.0 OD2 B:ASP136 4.4 41.5 1.0 CA B:CA301 4.4 45.1 1.0 CE1 B:HIS104 4.5 44.2 1.0 CB B:ASP100 4.5 41.8 1.0 CG B:GLU69 4.5 43.3 1.0 NE B:ARG68 4.5 46.1 1.0 NH2 B:ARG68 4.5 48.0 1.0 CB B:ASP103 4.5 42.6 1.0 N B:ASN102 4.6 40.3 1.0 CA B:ASP103 4.7 41.7 1.0 CA B:ASP100 4.7 41.6 1.0 C B:ASP100 4.7 41.1 1.0 CA B:ASN102 4.8 40.3 1.0 CG B:GLU11 4.8 39.5 1.0 C B:ASN102 4.9 40.4 1.0 C B:ASP103 5.0 41.5 1.0 CB B:GLN101 5.0 39.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human P-Cadherin (Int-X-Dimer)


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 (Int-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:40.5 occ:1.00 O B:HIS104 2.2 39.9 1.0 OD1 B:ASN102 2.3 40.4 1.0 OD2 B:ASP134 2.3 40.7 1.0 OD2 B:ASP195 2.3 38.0 1.0 OD2 B:ASP136 2.4 41.5 1.0 O B:ASN143 2.5 41.8 1.0 OD1 B:ASP134 2.7 40.5 1.0 CG B:ASP134 2.8 41.2 1.0 CG B:ASP195 3.3 38.3 1.0 CG B:ASP136 3.4 41.3 1.0 C B:HIS104 3.4 40.6 1.0 CG B:ASN102 3.5 41.1 1.0 C B:ASN143 3.6 42.2 1.0 CB B:ASP195 3.7 38.1 1.0 CB B:ASP136 3.8 41.4 1.0 ND2 B:ASN102 4.1 42.3 1.0 N B:HIS104 4.2 41.1 1.0 CA B:HIS104 4.2 41.3 1.0 CB B:ASP134 4.3 42.1 1.0 OD1 B:ASP195 4.3 39.2 1.0 CA B:ASN143 4.4 42.3 1.0 CB B:HIS104 4.4 41.7 1.0 N B:LYS105 4.5 40.3 1.0 OD1 B:ASP136 4.5 40.8 1.0 N B:GLY144 4.5 42.4 1.0 CB B:ASN143 4.6 41.9 1.0 CB B:ASN102 4.6 41.0 1.0 CA B:ASN102 4.7 40.3 1.0 CA B:LYS105 4.7 39.6 1.0 CA B:GLY144 4.7 42.7 1.0 C B:ASN102 4.9 40.4 1.0 C B:LYS105 4.9 39.2 1.0 N B:PRO106 4.9 38.6 1.0 N B:ASP136 5.0 42.4 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