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

The structure of Crystal Structure of Human P-Cadherin (Enc-X-Dimer), PDB code: 4zmw 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)	47.02 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.369, 106.810, 77.579, 90.00, 94.86, 90.00
R / Rfree (%)	23 / 27.6

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

Nickel

(Ni)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Enc-X-Dimer) (pdb code 4zmw). 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 (Enc-X-Dimer), PDB code: 4zmw:
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 (Enc-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 (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:17.3 occ:1.00 OD1 A:ASP100 2.3 20.5 1.0 OE2 A:GLU11 2.3 21.1 1.0 OD1 A:ASP103 2.3 29.1 1.0 OE2 A:GLU69 2.3 19.9 1.0 O A:GLN101 2.4 20.3 1.0 OD1 A:ASP136 2.4 18.4 1.0 OE1 A:GLU69 2.7 20.8 1.0 CD A:GLU69 2.8 22.0 1.0 CG A:ASP100 3.3 22.7 1.0 CG A:ASP136 3.3 18.8 1.0 CD A:GLU11 3.4 22.2 1.0 CG A:ASP103 3.4 22.8 1.0 C A:GLN101 3.6 20.3 1.0 OD2 A:ASP103 3.8 20.9 1.0 OD2 A:ASP100 3.8 19.8 1.0 N A:GLN101 3.8 18.6 1.0 OE1 A:GLU11 3.8 24.4 1.0 CB A:ASP136 3.9 18.6 1.0 N A:ASP103 4.1 23.8 1.0 CA A:ASP136 4.1 19.4 1.0 CG A:GLU69 4.3 23.3 1.0 OD2 A:ASP136 4.3 16.8 1.0 CA A:GLN101 4.4 19.3 1.0 NE A:ARG68 4.4 26.2 1.0 ND1 A:HIS104 4.4 26.3 1.0 CB A:ASP100 4.5 21.4 1.0 CA A:ASP100 4.6 21.1 1.0 NH2 A:ARG68 4.6 24.3 1.0 N A:ASN102 4.6 19.9 1.0 CB A:ASP103 4.7 22.7 1.0 CG A:GLU11 4.7 19.6 1.0 C A:ASP100 4.7 21.3 1.0 CA A:ASN102 4.8 19.0 1.0 CA A:ASP103 4.9 23.7 1.0 CE1 A:HIS104 4.9 24.9 1.0 N A:ASP136 4.9 19.2 1.0 CB A:ARG68 4.9 23.1 1.0 C A:ASN102 5.0 21.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin (Enc-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 (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:18.7 occ:1.00 OD2 A:ASP195 2.2 23.8 1.0 OD1 A:ASN102 2.2 17.7 1.0 O A:HIS104 2.2 23.5 1.0 OD2 A:ASP136 2.3 16.8 1.0 O A:ASN143 2.4 15.6 1.0 OD2 A:ASP134 2.4 20.6 1.0 OD1 A:ASP134 2.5 19.5 1.0 CG A:ASP134 2.8 18.6 1.0 CG A:ASP195 3.2 23.3 1.0 CG A:ASP136 3.3 18.8 1.0 CG A:ASN102 3.4 17.8 1.0 C A:HIS104 3.4 25.6 1.0 C A:ASN143 3.5 17.8 1.0 CB A:ASP195 3.6 23.7 1.0 CB A:ASP136 3.7 18.6 1.0 ND2 A:ASN102 4.0 18.7 1.0 O A:HOH405 4.1 44.8 1.0 OD1 A:ASP195 4.2 23.9 1.0 CA A:HIS104 4.2 24.4 1.0 CB A:ASP134 4.3 18.5 1.0 N A:HIS104 4.3 24.5 1.0 CA A:ASN143 4.3 18.8 1.0 N A:GLY144 4.4 18.1 1.0 N A:LYS105 4.4 27.9 1.0 OD1 A:ASP136 4.4 18.4 1.0 CB A:ASN143 4.5 17.1 1.0 CB A:HIS104 4.5 26.1 1.0 CA A:GLY144 4.5 18.3 1.0 CA A:LYS105 4.6 28.9 1.0 CB A:ASN102 4.6 18.9 1.0 CA A:ASN102 4.7 19.0 1.0 N A:ASP136 4.8 19.2 1.0 C A:LYS105 4.8 26.8 1.0 C A:ASN102 4.8 21.2 1.0 CA A:ASP136 4.9 19.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin (Enc-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 (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:18.9 occ:1.00 OD1 B:ASP136 2.2 21.0 1.0 OE2 B:GLU11 2.2 20.6 1.0 OD1 B:ASP100 2.3 18.9 1.0 OD1 B:ASP103 2.3 26.4 1.0 OE2 B:GLU69 2.3 25.3 1.0 O B:GLN101 2.4 21.2 1.0 OE1 B:GLU69 2.8 22.9 1.0 CD B:GLU69 2.9 25.4 1.0 CG B:ASP100 3.2 20.6 1.0 CG B:ASP136 3.3 22.3 1.0 CD B:GLU11 3.3 19.9 1.0 CG B:ASP103 3.4 27.9 1.0 C B:GLN101 3.6 23.1 1.0 OE1 B:GLU11 3.7 21.8 1.0 N B:GLN101 3.7 21.7 1.0 OD2 B:ASP100 3.8 20.0 1.0 OD2 B:ASP103 3.8 29.5 1.0 CB B:ASP136 3.9 22.7 1.0 CA B:ASP136 4.0 24.1 1.0 OD2 B:ASP136 4.2 21.8 1.0 N B:ASP103 4.2 27.4 1.0 CA B:GLN101 4.3 22.3 1.0 ND1 B:HIS104 4.4 28.5 1.0 CG B:GLU69 4.4 27.3 1.0 CB B:ASP100 4.4 21.2 1.0 NE B:ARG68 4.4 23.8 1.0 CA B:ASP100 4.5 20.8 1.0 CG B:GLU11 4.6 20.1 1.0 C B:ASP100 4.6 21.5 1.0 CB B:ASP103 4.7 26.0 1.0 N B:ASN102 4.7 22.7 1.0 NH2 B:ARG68 4.7 24.6 1.0 CB B:ARG68 4.8 23.9 1.0 N B:ASP136 4.9 24.4 1.0 CA B:ASN102 4.9 23.0 1.0 CA B:ASP103 5.0 26.5 1.0 N B:ASP137 5.0 25.7 1.0 CE1 B:HIS104 5.0 28.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin (Enc-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 (Enc-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:22.2 occ:1.00 OD1 B:ASN102 2.2 25.2 1.0 O B:HIS104 2.3 27.6 1.0 O B:ASN143 2.3 17.4 1.0 OD2 B:ASP195 2.3 22.7 1.0 OD2 B:ASP136 2.5 21.8 1.0 OD1 B:ASP134 2.6 17.3 1.0 OD2 B:ASP134 2.6 18.4 1.0 CG B:ASP134 3.0 19.0 1.0 CG B:ASP195 3.3 23.8 1.0 CG B:ASN102 3.4 23.1 1.0 CG B:ASP136 3.4 22.3 1.0 C B:HIS104 3.5 27.8 1.0 C B:ASN143 3.5 18.3 1.0 CB B:ASP195 3.6 24.8 1.0 CB B:ASP136 3.7 22.7 1.0 ND2 B:ASN102 4.0 22.5 1.0 O B:HOH407 4.0 20.6 1.0 CA B:HIS104 4.2 27.3 1.0 OD1 B:ASP195 4.3 24.9 1.0 N B:HIS104 4.3 27.1 1.0 CA B:ASN143 4.4 18.2 1.0 N B:GLY144 4.5 18.1 1.0 N B:LYS105 4.5 30.0 1.0 CB B:HIS104 4.5 27.6 1.0 CB B:ASP134 4.5 19.1 1.0 CA B:GLY144 4.6 18.7 1.0 CB B:ASN102 4.6 23.0 1.0 OD1 B:ASP136 4.6 21.0 1.0 CB B:ASN143 4.6 17.5 1.0 CA B:ASN102 4.6 23.0 1.0 CA B:LYS105 4.7 33.4 1.0 N B:ASP136 4.8 24.4 1.0 C B:LYS105 4.8 31.1 1.0 C B:ASN102 4.9 25.6 1.0 CA B:ASP136 4.9 24.1 1.0 N B:PRO106 4.9 28.4 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