Calcium in PDB 5jym: Human P-Cadherin EC12 with Scfv TSP11 Bound

The structure of Human P-Cadherin EC12 with Scfv TSP11 Bound, PDB code: 5jym 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)	99.91 / 2.45
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.700, 83.430, 199.820, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27

The binding sites of Calcium atom in the Human P-Cadherin EC12 with Scfv TSP11 Bound (pdb code 5jym). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Human P-Cadherin EC12 with Scfv TSP11 Bound, PDB code: 5jym:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.9 occ:1.00 OD2 A:ASP103 2.2 35.6 1.0 OE1 A:GLU69 2.2 31.7 1.0 OD1 A:ASP67 2.3 35.8 1.0 OE1 A:GLU11 2.3 33.5 1.0 O A:HOH411 2.4 30.1 1.0 CG A:ASP67 3.1 37.8 1.0 CG A:ASP103 3.1 36.1 1.0 CD A:GLU11 3.3 34.7 1.0 OD1 A:ASP103 3.5 32.9 1.0 CD A:GLU69 3.5 33.8 1.0 OD2 A:ASP67 3.7 38.2 1.0 OE2 A:GLU11 3.8 36.2 1.0 CB A:ASP67 4.1 36.8 1.0 N A:ARG68 4.2 34.5 1.0 O A:HOH434 4.2 41.4 1.0 N A:GLU69 4.2 37.0 1.0 CB A:GLU69 4.2 36.7 1.0 CA A:ASP67 4.2 35.3 1.0 CE1 A:HIS104 4.3 42.5 1.0 OE2 A:GLU69 4.3 30.7 1.0 CA A:CA302 4.3 34.2 1.0 OD1 A:ASN12 4.4 35.1 1.0 CG A:GLU69 4.4 34.1 1.0 CB A:ASP103 4.5 37.2 1.0 C A:ASP67 4.5 34.2 1.0 ND2 A:ASN12 4.6 34.9 1.0 CG A:GLU11 4.6 35.7 1.0 ND1 A:HIS104 4.9 44.5 1.0 CG A:ASN12 4.9 34.5 1.0 CA A:GLU69 4.9 38.6 1.0

Calcium binding site 2 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:34.2 occ:1.00 OD1 A:ASP100 2.1 34.4 1.0 OE2 A:GLU69 2.2 30.7 1.0 O A:GLN101 2.2 32.3 1.0 OD1 A:ASP103 2.3 32.9 1.0 OD1 A:ASP136 2.4 37.4 1.0 OE2 A:GLU11 2.4 36.2 1.0 CD A:GLU69 3.0 33.8 1.0 OE1 A:GLU69 3.0 31.7 1.0 CG A:ASP100 3.2 36.7 1.0 CG A:ASP103 3.4 36.1 1.0 CG A:ASP136 3.4 39.2 1.0 C A:GLN101 3.5 36.1 1.0 CD A:GLU11 3.5 34.7 1.0 OD2 A:ASP100 3.7 36.8 1.0 N A:GLN101 3.8 34.5 1.0 OE1 A:GLU11 3.9 33.5 1.0 N A:ASP103 3.9 38.8 1.0 OD2 A:ASP103 4.0 35.6 1.0 CB A:ASP136 4.1 39.2 1.0 ND1 A:HIS104 4.2 44.5 1.0 CA A:GLN101 4.3 36.4 1.0 CA A:ASP136 4.3 40.5 1.0 CA A:CA301 4.3 37.9 1.0 OD2 A:ASP136 4.3 40.6 1.0 NE A:ARG68 4.4 39.9 1.0 CG A:GLU69 4.4 34.1 1.0 CB A:ASP100 4.5 34.5 1.0 N A:ASN102 4.5 37.3 1.0 NH2 A:ARG68 4.5 40.5 1.0 CB A:ASP103 4.6 37.2 1.0 CA A:ASP100 4.6 33.1 1.0 C A:ASP100 4.7 32.8 1.0 CA A:ASP103 4.7 39.0 1.0 CA A:ASN102 4.7 37.9 1.0 CE1 A:HIS104 4.8 42.5 1.0 CG A:GLU11 4.8 35.7 1.0 C A:ASN102 4.8 36.7 1.0 N A:HIS104 5.0 40.7 1.0 CZ A:ARG68 5.0 38.3 1.0 CB A:GLN101 5.0 39.5 1.0

Calcium binding site 3 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:37.8 occ:1.00 OD1 A:ASN102 2.3 42.9 1.0 OD2 A:ASP136 2.3 40.6 1.0 O A:ASN143 2.3 37.7 1.0 O A:HIS104 2.3 40.5 1.0 OD1 A:ASP134 2.4 50.5 1.0 OD2 A:ASP195 2.5 34.6 1.0 OD2 A:ASP134 2.6 49.0 1.0 CG A:ASP134 2.9 47.4 1.0 CG A:ASP136 3.3 39.2 1.0 CG A:ASN102 3.4 39.2 1.0 CG A:ASP195 3.4 34.7 1.0 C A:ASN143 3.5 39.0 1.0 C A:HIS104 3.5 43.0 1.0 CB A:ASP136 3.7 39.2 1.0 CB A:ASP195 3.8 35.5 1.0 ND2 A:ASN102 4.1 40.4 1.0 CA A:HIS104 4.2 43.3 1.0 N A:HIS104 4.3 40.7 1.0 CA A:ASN143 4.3 39.2 1.0 CB A:ASP134 4.4 44.6 1.0 N A:GLY144 4.4 36.9 1.0 OD1 A:ASP136 4.4 37.4 1.0 CB A:HIS104 4.4 41.9 1.0 CB A:ASN143 4.5 38.8 1.0 CA A:GLY144 4.5 38.1 1.0 OD1 A:ASP195 4.5 35.6 1.0 N A:LYS105 4.5 45.5 1.0 CB A:ASN102 4.6 39.0 1.0 CA A:ASN102 4.7 37.9 1.0 CA A:LYS105 4.8 48.3 1.0 N A:ASP136 4.8 41.6 1.0 C A:ASN102 4.8 36.7 1.0 CA A:ASP136 4.9 40.5 1.0 C A:LYS105 5.0 48.1 1.0 CD A:PRO106 5.0 46.6 1.0

Calcium binding site 4 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:59.4 occ:1.00 O A:ASP44 2.5 39.9 1.0 O A:HOH433 2.7 44.3 1.0 C A:ASP44 3.7 36.1 1.0 O B:TYR102 4.2 42.8 1.0 CB A:ASP44 4.4 35.8 1.0 CA A:ASP44 4.4 34.6 1.0 N A:SER45 4.6 36.5 1.0 CA A:SER45 4.7 37.6 1.0 CG A:ASP44 4.8 36.2 1.0 CB A:SER45 4.9 36.6 1.0 O A:HOH440 4.9 19.4 0.5

Calcium binding site 5 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:33.5 occ:1.00 OD1 C:ASP100 2.1 36.6 1.0 OD1 C:ASP103 2.2 31.9 1.0 OE2 C:GLU69 2.2 31.6 1.0 O C:GLN101 2.3 34.1 1.0 OE2 C:GLU11 2.4 35.1 1.0 OD1 C:ASP136 2.5 38.4 1.0 CD C:GLU69 2.9 36.6 1.0 OE1 C:GLU69 3.0 38.0 1.0 CG C:ASP100 3.2 36.7 1.0 CG C:ASP103 3.3 34.1 1.0 CD C:GLU11 3.5 34.0 1.0 C C:GLN101 3.5 34.4 1.0 CG C:ASP136 3.5 39.4 1.0 OD2 C:ASP100 3.8 39.9 1.0 OD2 C:ASP103 3.8 36.5 1.0 N C:GLN101 3.8 32.2 1.0 OE1 C:GLU11 3.8 33.2 1.0 N C:ASP103 3.9 34.3 1.0 CD2 C:HIS104 4.1 39.4 1.0 CB C:ASP136 4.2 39.8 1.0 CA C:CA303 4.3 35.3 1.0 CA C:GLN101 4.3 33.9 1.0 CA C:ASP136 4.4 39.4 1.0 CG C:GLU69 4.4 35.6 1.0 NE C:ARG68 4.4 37.7 1.0 CB C:ASP100 4.4 34.9 1.0 OD2 C:ASP136 4.5 41.0 1.0 CB C:ASP103 4.5 34.0 1.0 N C:ASN102 4.5 34.8 1.0 CA C:ASP100 4.6 32.1 1.0 NH2 C:ARG68 4.6 34.5 1.0 CA C:ASP103 4.6 34.5 1.0 C C:ASP100 4.7 31.7 1.0 CA C:ASN102 4.7 35.5 1.0 NE2 C:HIS104 4.8 41.1 1.0 CG C:GLU11 4.8 34.5 1.0 C C:ASN102 4.8 34.5 1.0 CB C:GLN101 5.0 36.2 1.0 N C:HIS104 5.0 35.6 1.0

Calcium binding site 6 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:35.4 occ:1.00 OD1 C:ASN102 2.2 42.6 1.0 O C:HIS104 2.2 34.7 1.0 OD2 C:ASP136 2.3 41.0 1.0 O C:ASN143 2.4 52.1 1.0 OD2 C:ASP195 2.4 36.6 1.0 OD1 C:ASP134 2.5 46.0 1.0 OD2 C:ASP134 2.6 41.2 1.0 CG C:ASP134 2.9 39.5 1.0 CG C:ASP136 3.3 39.4 1.0 CG C:ASN102 3.4 39.6 1.0 C C:HIS104 3.4 36.7 1.0 CG C:ASP195 3.4 41.1 1.0 C C:ASN143 3.6 52.1 1.0 CB C:ASP136 3.8 39.8 1.0 CB C:ASP195 3.8 40.4 1.0 ND2 C:ASN102 4.0 40.5 1.0 CA C:HIS104 4.2 37.1 1.0 N C:HIS104 4.3 35.6 1.0 CA C:ASN143 4.4 59.1 1.0 CB C:ASP134 4.4 39.0 1.0 CB C:HIS104 4.4 35.6 1.0 N C:LYS105 4.4 39.4 1.0 OD1 C:ASP136 4.4 38.4 1.0 CB C:ASN143 4.5 62.0 1.0 N C:GLY144 4.5 47.0 1.0 OD1 C:ASP195 4.5 40.1 1.0 CB C:ASN102 4.6 36.7 1.0 CA C:GLY144 4.6 48.1 1.0 CA C:ASN102 4.6 35.5 1.0 CA C:LYS105 4.6 40.2 1.0 N C:ASP136 4.8 38.5 1.0 C C:ASN102 4.8 34.5 1.0 C C:LYS105 4.9 38.9 1.0 CA C:ASP136 4.9 39.4 1.0 CD C:PRO106 5.0 40.6 1.0

Calcium binding site 7 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:35.3 occ:1.00 OD2 C:ASP103 2.2 36.5 1.0 O C:HOH408 2.3 27.3 1.0 OE1 C:GLU69 2.3 38.0 1.0 O C:HOH433 2.4 31.2 1.0 OE1 C:GLU11 2.4 33.2 1.0 OD1 C:ASP67 2.4 33.6 1.0 CG C:ASP103 3.2 34.1 1.0 CG C:ASP67 3.3 37.6 1.0 CD C:GLU11 3.4 34.0 1.0 OD1 C:ASP103 3.5 31.9 1.0 CD C:GLU69 3.5 36.6 1.0 OD2 C:ASP67 3.8 44.9 1.0 OE2 C:GLU11 3.9 35.1 1.0 OD1 C:ASN12 4.2 27.6 1.0 CB C:GLU69 4.3 37.7 1.0 CB C:ASP67 4.3 35.1 1.0 CA C:CA301 4.3 33.5 1.0 N C:ARG68 4.4 30.7 1.0 N C:GLU69 4.4 38.2 1.0 CA C:ASP67 4.4 32.8 1.0 OE2 C:GLU69 4.4 31.6 1.0 CG C:GLU69 4.4 35.6 1.0 NE2 C:HIS104 4.4 41.1 1.0 ND2 C:ASN12 4.5 31.9 1.0 CB C:ASP103 4.5 34.0 1.0 C C:ASP67 4.6 30.1 1.0 CG C:GLU11 4.6 34.5 1.0 CG C:ASN12 4.8 29.1 1.0 CA C:GLU69 5.0 39.6 1.0 CD2 C:HIS104 5.0 39.4 1.0

Calcium binding site 8 out of 8 in the Human P-Cadherin EC12 with Scfv TSP11 Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human P-Cadherin EC12 with Scfv TSP11 Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:84.2 occ:1.00 O C:THR109 2.5 50.3 1.0 C C:THR109 3.7 45.5 1.0 CA C:THR109 4.5 41.9 1.0 N C:GLN110 4.6 46.1 1.0 CA C:GLN110 4.7 48.4 1.0

S.Kudo, J.M.M.Caaveiro, S.Nagatoishi, T.Miyafusa, T.Matsuura, Y.Sudou, K.Tsumoto. Disruption of Cell Adhesion By An Antibody Targeting the Cell-Adhesive Intermediate (X-Dimer) of Human P-Cadherin Sci Rep V. 7 39518 2017.
ISSN: ESSN 2045-2322
PubMed: 28045038
DOI: 10.1038/SREP39518