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

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer), PDB code: 4zmq 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)	39.72 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	182.090, 182.090, 41.040, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 23.1

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer) (pdb code 4zmq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer), PDB code: 4zmq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.3 occ:1.00 OD2 A:ASP103 2.2 30.2 1.0 O A:HOH431 2.3 31.1 1.0 OD1 A:ASP67 2.3 33.7 1.0 OE1 A:GLU69 2.3 32.1 1.0 OE1 A:GLU11 2.3 31.1 1.0 O A:HOH500 2.5 29.5 1.0 CG A:ASP103 3.2 29.4 1.0 CD A:GLU11 3.3 31.4 1.0 CG A:ASP67 3.3 35.6 1.0 OD1 A:ASP103 3.4 29.3 1.0 CD A:GLU69 3.5 31.8 1.0 OE2 A:GLU11 3.7 31.5 1.0 OD2 A:ASP67 4.0 38.6 1.0 CA A:CA302 4.1 30.1 1.0 N A:ARG68 4.2 33.6 1.0 N A:GLU69 4.3 34.8 1.0 CA A:ASP67 4.3 34.4 1.0 ND2 A:ASN12 4.3 34.3 1.0 CB A:GLU69 4.3 33.9 1.0 NE2 A:HIS104 4.3 36.8 1.0 CB A:ASP67 4.3 35.1 1.0 OD1 A:ASN12 4.3 35.8 1.0 OE2 A:GLU69 4.4 33.3 1.0 CG A:GLU69 4.4 32.3 1.0 C A:ASP67 4.5 33.5 1.0 CB A:ASP103 4.6 28.5 1.0 CG A:GLU11 4.6 31.4 1.0 CG A:ASN12 4.7 35.4 1.0 CD2 A:HIS104 4.9 36.5 1.0 CA A:GLU69 4.9 36.5 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.1 occ:1.00 OD1 A:ASP103 2.3 29.3 1.0 OE2 A:GLU11 2.4 31.5 1.0 OD1 A:ASP100 2.4 32.1 1.0 OD1 A:ASP136 2.4 27.0 1.0 OE2 A:GLU69 2.4 33.3 1.0 O A:GLN101 2.5 29.6 1.0 OE1 A:GLU69 2.8 32.1 1.0 CD A:GLU69 3.0 31.8 1.0 CG A:ASP100 3.2 31.2 1.0 CG A:ASP103 3.4 29.4 1.0 CD A:GLU11 3.5 31.4 1.0 CG A:ASP136 3.5 27.9 1.0 OD2 A:ASP100 3.5 29.0 1.0 C A:GLN101 3.7 28.2 1.0 OE1 A:GLU11 3.9 31.1 1.0 N A:GLN101 3.9 31.1 1.0 OD2 A:ASP103 3.9 30.2 1.0 N A:ASP103 4.0 26.9 1.0 CB A:ASP136 4.1 28.1 1.0 CD2 A:HIS104 4.1 36.5 1.0 CA A:CA301 4.1 34.3 1.0 CA A:ASP136 4.3 29.8 1.0 NE A:ARG68 4.4 34.1 1.0 CA A:GLN101 4.4 28.5 1.0 OD2 A:ASP136 4.5 27.8 1.0 CB A:ASP100 4.5 31.9 1.0 CG A:GLU69 4.5 32.3 1.0 CB A:ASP103 4.6 28.5 1.0 N A:ASN102 4.7 28.1 1.0 CA A:ASP100 4.7 31.5 1.0 NE2 A:HIS104 4.7 36.8 1.0 NH2 A:ARG68 4.7 36.7 1.0 CG A:GLU11 4.7 31.4 1.0 CA A:ASP103 4.8 29.4 1.0 C A:ASP100 4.8 31.6 1.0 CA A:ASN102 4.8 27.4 1.0 C A:ASN102 5.0 28.1 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:26.2 occ:1.00 O A:HIS104 2.3 29.6 1.0 OD1 A:ASN102 2.3 27.0 1.0 OD2 A:ASP136 2.3 27.8 1.0 O A:ASN143 2.4 23.1 1.0 OD2 A:ASP195 2.4 26.3 1.0 OD2 A:ASP134 2.4 27.4 1.0 OD1 A:ASP134 2.5 28.1 1.0 CG A:ASP134 2.8 27.3 1.0 CG A:ASP136 3.4 27.9 1.0 CG A:ASP195 3.4 24.9 1.0 CG A:ASN102 3.5 26.8 1.0 C A:HIS104 3.5 33.3 1.0 C A:ASN143 3.5 24.8 1.0 CB A:ASP195 3.7 24.3 1.0 CB A:ASP136 3.8 28.1 1.0 ND2 A:ASN102 4.0 25.9 1.0 O A:HOH437 4.2 30.3 1.0 CA A:HIS104 4.3 34.5 1.0 N A:HIS104 4.3 33.7 1.0 CB A:ASP134 4.3 27.0 1.0 CA A:ASN143 4.3 24.3 1.0 N A:GLY144 4.4 25.5 1.0 CB A:ASN143 4.5 25.1 1.0 N A:LYS105 4.5 33.0 1.0 CB A:HIS104 4.5 34.5 1.0 OD1 A:ASP136 4.5 27.0 1.0 OD1 A:ASP195 4.5 25.5 1.0 CA A:GLY144 4.5 25.7 1.0 CA A:LYS105 4.6 33.8 1.0 CB A:ASN102 4.7 27.3 1.0 CA A:ASN102 4.7 27.4 1.0 N A:ASP136 4.8 30.4 1.0 C A:LYS105 4.8 29.9 1.0 C A:ASN102 4.9 28.1 1.0 CA A:ASP136 4.9 29.8 1.0 CD A:PRO106 4.9 25.3 1.0 N A:PRO106 4.9 26.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:60.5 occ:1.00 O A:GLU69 2.6 39.9 1.0 O A:HOH444 2.6 47.5 1.0 C A:GLU69 3.8 38.2 1.0 O A:GLU70 4.4 47.8 1.0 CA A:GLU70 4.5 44.9 1.0 N A:GLU70 4.6 40.7 1.0 CA A:GLU69 4.8 36.5 1.0 C A:GLU70 4.8 45.2 1.0 O A:HOH506 5.0 45.2 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:65.8 occ:1.00 OD1 A:ASP213 2.7 55.2 1.0 OXT A:ASP213 3.5 42.7 1.0 CA A:ASP213 4.0 44.7 1.0 CG A:ASP213 4.0 55.9 1.0 C A:ASP213 4.2 43.5 1.0 O A:HOH468 4.5 34.2 1.0 CB A:ASP213 4.6 48.9 1.0 O A:LEU212 4.6 36.3 1.0 OD2 A:ASP213 5.0 61.0 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-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 (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:26.3 occ:1.00 OE1 B:GLU69 2.2 27.9 1.0 OD1 B:ASP67 2.2 29.3 1.0 OD2 B:ASP103 2.3 28.5 1.0 OE1 B:GLU11 2.3 28.2 1.0 O B:HOH420 2.3 26.0 1.0 O B:HOH484 2.3 28.4 1.0 CG B:ASP103 3.1 26.8 1.0 CG B:ASP67 3.2 29.7 1.0 CD B:GLU11 3.3 29.3 1.0 OD1 B:ASP103 3.3 26.7 1.0 CD B:GLU69 3.5 27.1 1.0 OE2 B:GLU11 3.7 29.7 1.0 OD2 B:ASP67 3.9 30.2 1.0 CA B:CA302 4.1 28.2 1.0 CB B:ASP67 4.2 30.0 1.0 NE2 B:HIS104 4.2 35.3 1.0 CA B:ASP67 4.2 28.0 1.0 N B:ARG68 4.2 29.1 1.0 OE2 B:GLU69 4.3 26.4 1.0 ND2 B:ASN12 4.3 29.6 1.0 OD1 B:ASN12 4.3 31.0 1.0 N B:GLU69 4.3 31.5 1.0 CB B:GLU69 4.4 30.1 1.0 CG B:GLU69 4.4 29.4 1.0 C B:ASP67 4.5 27.4 1.0 CB B:ASP103 4.5 26.5 1.0 CG B:GLU11 4.6 27.3 1.0 CG B:ASN12 4.8 28.3 1.0 CD2 B:HIS104 4.8 32.8 1.0 CB B:GLU11 5.0 27.5 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:28.2 occ:1.00 OD1 B:ASP100 2.3 31.2 1.0 OD1 B:ASP103 2.3 26.7 1.0 O B:GLN101 2.3 25.8 1.0 OD1 B:ASP136 2.3 30.4 1.0 OE2 B:GLU69 2.3 26.4 1.0 OE2 B:GLU11 2.4 29.7 1.0 OE1 B:GLU69 2.9 27.9 1.0 CD B:GLU69 3.0 27.1 1.0 CG B:ASP100 3.2 32.1 1.0 CG B:ASP136 3.4 31.6 1.0 CD B:GLU11 3.4 29.3 1.0 CG B:ASP103 3.4 26.8 1.0 C B:GLN101 3.5 26.4 1.0 OD2 B:ASP100 3.7 29.3 1.0 OE1 B:GLU11 3.8 28.2 1.0 N B:GLN101 3.8 24.8 1.0 N B:ASP103 4.0 26.7 1.0 OD2 B:ASP103 4.0 28.5 1.0 CD2 B:HIS104 4.0 32.8 1.0 CB B:ASP136 4.0 31.0 1.0 CA B:CA301 4.1 26.3 1.0 CA B:ASP136 4.3 31.1 1.0 OD2 B:ASP136 4.3 31.5 1.0 CA B:GLN101 4.3 24.9 1.0 CG B:GLU69 4.4 29.4 1.0 CB B:ASP100 4.5 30.0 1.0 NE B:ARG68 4.5 33.4 1.0 CB B:ASP103 4.6 26.5 1.0 N B:ASN102 4.6 24.8 1.0 CA B:ASP100 4.6 28.8 1.0 NH2 B:ARG68 4.6 34.9 1.0 NE2 B:HIS104 4.6 35.3 1.0 CA B:ASP103 4.7 29.0 1.0 C B:ASP100 4.7 26.0 1.0 CG B:GLU11 4.7 27.3 1.0 CA B:ASN102 4.8 25.9 1.0 C B:ASN102 4.9 24.4 1.0 CB B:GLN101 4.9 28.0 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:29.4 occ:1.00 OD1 B:ASN102 2.3 29.8 1.0 O B:HIS104 2.3 27.8 1.0 O B:ASN143 2.4 28.5 1.0 OD2 B:ASP136 2.4 31.5 1.0 OD1 B:ASP134 2.4 31.5 1.0 OD2 B:ASP195 2.5 26.6 1.0 OD2 B:ASP134 2.5 32.4 1.0 CG B:ASP134 2.8 32.3 1.0 CG B:ASN102 3.4 25.9 1.0 CG B:ASP195 3.4 27.3 1.0 CG B:ASP136 3.5 31.6 1.0 C B:HIS104 3.5 30.6 1.0 C B:ASN143 3.6 29.3 1.0 CB B:ASP195 3.7 28.0 1.0 CB B:ASP136 3.8 31.0 1.0 ND2 B:ASN102 3.9 25.4 1.0 N B:HIS104 4.2 32.8 1.0 O B:HOH406 4.2 26.0 1.0 CA B:HIS104 4.2 34.0 1.0 CB B:ASP134 4.3 31.8 1.0 CA B:ASN143 4.4 29.3 1.0 N B:GLY144 4.5 29.8 1.0 OD1 B:ASP195 4.5 28.4 1.0 CB B:ASN143 4.5 27.0 1.0 N B:LYS105 4.5 29.5 1.0 CB B:HIS104 4.5 32.7 1.0 OD1 B:ASP136 4.6 30.4 1.0 CB B:ASN102 4.6 25.9 1.0 CA B:GLY144 4.6 30.7 1.0 CA B:ASN102 4.7 25.9 1.0 CA B:LYS105 4.7 34.4 1.0 C B:ASN102 4.8 24.4 1.0 C B:LYS105 4.9 33.5 1.0 N B:ASP136 4.9 33.7 1.0 N B:PRO106 4.9 33.2 1.0 CD B:PRO106 4.9 33.3 1.0 CA B:ASP136 5.0 31.1 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