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

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I), PDB code: 4zmv 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)	45.10 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.440, 98.910, 109.980, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.6

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

Nickel

(Ni)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I) (pdb code 4zmv). 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 (Ss-X-Dimer Pocket I), PDB code: 4zmv:
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 (Ss-X-Dimer Pocket I)


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 Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.6 occ:1.00 OD1 A:ASN102 2.2 33.5 1.0 OD2 A:ASP134 2.4 45.8 1.0 O A:ASN143 2.4 33.2 1.0 O A:HIS104 2.4 44.1 1.0 OD2 A:ASP195 2.4 32.6 1.0 OD2 A:ASP136 2.5 40.8 1.0 OD1 A:ASP134 2.5 37.4 1.0 CG A:ASP134 2.8 41.3 1.0 CG A:ASP195 3.4 35.0 1.0 CG A:ASN102 3.4 32.8 1.0 CG A:ASP136 3.5 38.5 1.0 C A:HIS104 3.5 42.2 1.0 C A:ASN143 3.6 34.1 1.0 CB A:ASP195 3.8 34.5 1.0 CB A:ASP136 3.8 36.6 1.0 ND2 A:ASN102 4.1 31.7 1.0 N A:HIS104 4.2 39.5 1.0 CA A:HIS104 4.2 40.6 1.0 CB A:ASP134 4.4 39.5 1.0 CB A:HIS104 4.4 40.6 1.0 N A:GLY144 4.5 33.9 1.0 CA A:ASN143 4.5 35.1 1.0 OD1 A:ASP136 4.5 42.5 1.0 OD1 A:ASP195 4.5 36.6 1.0 CA A:GLY144 4.6 32.8 1.0 N A:LYS105 4.6 46.0 1.0 CA A:ASN102 4.6 30.9 1.0 CB A:ASN143 4.6 33.6 1.0 CB A:ASN102 4.6 31.8 1.0 CA A:LYS105 4.8 48.9 1.0 C A:ASN102 4.8 30.0 1.0 N A:ASP136 4.9 36.7 1.0 C A:LYS105 4.9 45.4 1.0 N A:PRO106 5.0 43.0 1.0 O A:ASN102 5.0 29.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:35.8 occ:1.00 OD2 A:ASP103 2.2 30.4 1.0 OE2 A:GLU69 2.2 33.0 1.0 O A:GLN101 2.3 32.4 1.0 OE2 A:GLU11 2.3 38.1 1.0 OD1 A:ASP136 2.4 42.5 1.0 OD2 A:ASP100 2.5 29.5 1.0 OE1 A:GLU69 2.8 40.6 1.0 CD A:GLU69 2.8 40.3 1.0 CG A:ASP136 3.2 38.5 1.0 CG A:ASP103 3.3 32.3 1.0 CG A:ASP100 3.3 32.2 1.0 CD A:GLU11 3.4 34.6 1.0 C A:GLN101 3.5 34.0 1.0 OD1 A:ASP100 3.7 31.4 1.0 OD1 A:ASP103 3.7 35.1 1.0 CB A:ASP136 3.8 36.6 1.0 N A:GLN101 3.8 33.0 1.0 OE1 A:GLU11 3.9 32.7 1.0 N A:ASP103 4.0 31.2 1.0 OD2 A:ASP136 4.1 40.8 1.0 CA A:ASP136 4.1 36.6 1.0 ND1 A:HIS104 4.2 41.2 1.0 CG A:GLU69 4.3 41.0 1.0 CA A:GLN101 4.3 34.2 1.0 NE A:ARG68 4.4 37.9 1.0 CB A:ASP100 4.5 34.3 1.0 NH2 A:ARG68 4.5 36.4 1.0 N A:ASN102 4.5 30.8 1.0 CB A:ASP103 4.5 32.5 1.0 CA A:ASP100 4.6 33.1 1.0 CE1 A:HIS104 4.7 41.7 1.0 C A:ASP100 4.7 33.8 1.0 CG A:GLU11 4.7 34.5 1.0 CA A:ASN102 4.8 30.9 1.0 CA A:ASP103 4.8 33.5 1.0 C A:ASN102 4.9 30.0 1.0 N A:ASP136 5.0 36.7 1.0 CZ A:ARG68 5.0 37.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer Pocket I)


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 Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:34.2 occ:1.00 OD2 B:ASP103 2.1 35.5 1.0 OD2 B:ASP100 2.3 32.9 1.0 OE2 B:GLU11 2.4 33.4 1.0 OD1 B:ASP136 2.4 38.5 1.0 O B:GLN101 2.4 31.8 1.0 OE2 B:GLU69 2.5 38.1 1.0 OE1 B:GLU69 2.7 40.4 1.0 CD B:GLU69 2.9 42.5 1.0 CG B:ASP136 3.2 37.0 1.0 CG B:ASP103 3.2 40.7 1.0 CG B:ASP100 3.3 36.8 1.0 CD B:GLU11 3.4 37.6 1.0 C B:GLN101 3.6 35.5 1.0 OE1 B:GLU11 3.7 39.6 1.0 OD1 B:ASP103 3.8 44.0 1.0 CB B:ASP136 3.8 35.2 1.0 OD1 B:ASP100 3.9 34.7 1.0 N B:GLN101 3.9 34.5 1.0 ND1 B:HIS104 4.0 45.6 1.0 OD2 B:ASP136 4.0 40.1 1.0 N B:ASP103 4.0 38.0 1.0 CA B:ASP136 4.1 35.2 1.0 CE1 B:HIS104 4.4 48.7 1.0 CA B:GLN101 4.4 36.9 1.0 CG B:GLU69 4.4 45.0 1.0 CB B:ASP103 4.5 39.8 1.0 CB B:ASP100 4.6 33.5 1.0 N B:ASN102 4.6 35.9 1.0 NE B:ARG68 4.7 35.1 1.0 CA B:ASP100 4.7 33.1 1.0 CA B:ASP103 4.7 38.9 1.0 CG B:GLU11 4.7 36.5 1.0 NH2 B:ARG68 4.8 36.0 1.0 CA B:ASN102 4.8 36.8 1.0 C B:ASP100 4.8 33.3 1.0 N B:ASP136 4.9 36.3 1.0 C B:ASN102 4.9 38.1 1.0

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


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 Pocket I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:42.7 occ:1.00 OD1 B:ASN102 2.1 41.1 1.0 O B:HIS104 2.3 45.9 1.0 OD2 B:ASP134 2.4 42.6 1.0 O B:ASN143 2.4 34.3 1.0 OD2 B:ASP195 2.5 30.4 1.0 OD1 B:ASP134 2.5 41.9 1.0 OD2 B:ASP136 2.6 40.1 1.0 CG B:ASP134 2.8 42.9 1.0 CG B:ASN102 3.3 41.8 1.0 CG B:ASP195 3.3 32.9 1.0 C B:HIS104 3.5 45.9 1.0 CG B:ASP136 3.6 37.0 1.0 C B:ASN143 3.6 35.5 1.0 CB B:ASP195 3.7 32.4 1.0 ND2 B:ASN102 3.9 40.8 1.0 CB B:ASP136 4.0 35.2 1.0 O B:HOH411 4.1 37.9 1.0 CA B:HIS104 4.3 44.4 1.0 N B:HIS104 4.3 40.5 1.0 CB B:ASP134 4.3 40.4 1.0 OD1 B:ASP195 4.4 35.0 1.0 CA B:ASN143 4.4 37.6 1.0 N B:LYS105 4.5 49.9 1.0 CB B:ASN102 4.5 37.9 1.0 N B:GLY144 4.5 36.1 1.0 CA B:ASN102 4.6 36.8 1.0 CB B:HIS104 4.6 45.4 1.0 OD1 B:ASP136 4.6 38.5 1.0 CA B:GLY144 4.6 34.7 1.0 CA B:LYS105 4.6 51.4 1.0 CB B:ASN143 4.6 38.3 1.0 C B:LYS105 4.7 44.5 1.0 C B:ASN102 4.8 38.1 1.0 N B:PRO106 4.8 41.3 1.0 N B:ASP136 5.0 36.3 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