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

The structure of Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long), PDB code: 4zmt 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)	42.31 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.210, 105.830, 90.210, 90.00, 96.80, 90.00
R / Rfree (%)	22.8 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long) (pdb code 4zmt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long), PDB code: 4zmt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:39.8 occ:1.00 OD2 A:ASP103 2.3 35.2 1.0 OE1 A:GLU69 2.3 31.0 1.0 OD1 A:ASP67 2.4 35.8 1.0 OE1 A:GLU11 2.5 39.6 1.0 CG A:ASP67 3.1 35.2 1.0 CG A:ASP103 3.3 34.4 1.0 CD A:GLU11 3.5 35.7 1.0 CD A:GLU69 3.5 33.5 1.0 OD1 A:ASP103 3.6 35.4 1.0 OD2 A:ASP67 3.7 36.4 1.0 OE2 A:GLU11 3.9 37.1 1.0 CB A:ASP67 4.0 34.2 1.0 OD1 A:ASN12 4.1 37.0 1.0 CA A:ASP67 4.1 32.8 1.0 ND2 A:ASN12 4.2 36.3 1.0 N A:ARG68 4.3 31.8 1.0 CB A:GLU69 4.3 33.9 1.0 NE2 A:HIS104 4.4 39.5 1.0 N A:GLU69 4.4 33.9 1.0 CG A:GLU69 4.4 33.2 1.0 OE2 A:GLU69 4.4 33.8 1.0 CA A:CA302 4.5 28.1 1.0 C A:ASP67 4.5 31.7 1.0 CB A:ASP103 4.6 35.1 1.0 CG A:ASN12 4.6 35.4 1.0 CG A:GLU11 4.7 34.9 1.0 CD2 A:HIS104 4.8 37.0 1.0

Calcium binding site 2 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:28.1 occ:1.00 OD1 A:ASP100 2.1 32.6 1.0 OE2 A:GLU69 2.3 33.8 1.0 OE2 A:GLU11 2.3 37.1 1.0 O A:GLN101 2.3 32.2 1.0 OD1 A:ASP103 2.4 35.4 1.0 OD1 A:ASP136 2.4 30.9 1.0 CD A:GLU69 3.0 33.5 1.0 OE1 A:GLU69 3.1 31.0 1.0 CG A:ASP100 3.2 33.6 1.0 CG A:ASP103 3.4 34.4 1.0 CD A:GLU11 3.4 35.7 1.0 CG A:ASP136 3.4 31.8 1.0 C A:GLN101 3.5 33.6 1.0 OD2 A:ASP100 3.7 36.3 1.0 N A:GLN101 3.7 32.8 1.0 OD2 A:ASP103 3.8 35.2 1.0 OE1 A:GLU11 3.9 39.6 1.0 N A:ASP103 4.0 34.7 1.0 CB A:ASP136 4.1 33.0 1.0 CA A:GLN101 4.2 33.3 1.0 CA A:ASP136 4.2 35.0 1.0 CD2 A:HIS104 4.3 37.0 1.0 CB A:ASP100 4.4 33.1 1.0 OD2 A:ASP136 4.4 31.9 1.0 CG A:GLU69 4.4 33.2 1.0 NE A:ARG68 4.4 30.1 1.0 CA A:CA301 4.5 39.8 1.0 CA A:ASP100 4.5 32.4 1.0 CB A:ASP103 4.6 35.1 1.0 C A:ASP100 4.6 32.0 1.0 N A:ASN102 4.6 33.6 1.0 NH2 A:ARG68 4.7 30.6 1.0 CG A:GLU11 4.7 34.9 1.0 CA A:ASP103 4.8 35.1 1.0 CB A:GLN101 4.8 34.0 1.0 CA A:ASN102 4.8 33.7 1.0 C A:ASN102 4.9 34.4 1.0

Calcium binding site 3 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:32.3 occ:1.00 OD1 A:ASN102 2.2 34.4 1.0 O A:HIS104 2.3 35.3 1.0 O A:ASN143 2.4 29.5 1.0 OD2 A:ASP136 2.4 31.9 1.0 OD1 A:ASP134 2.4 29.5 1.0 OD2 A:ASP134 2.5 33.0 1.0 OD2 A:ASP195 2.6 30.3 1.0 CG A:ASP134 2.8 32.2 1.0 CG A:ASN102 3.4 34.0 1.0 CG A:ASP136 3.4 31.8 1.0 C A:ASN143 3.5 29.4 1.0 CG A:ASP195 3.5 31.0 1.0 C A:HIS104 3.5 35.3 1.0 CB A:ASP195 3.8 30.2 1.0 CB A:ASP136 3.8 33.0 1.0 ND2 A:ASN102 4.0 35.9 1.0 CA A:HIS104 4.3 35.2 1.0 CB A:ASP134 4.3 33.8 1.0 N A:HIS104 4.3 34.9 1.0 CA A:ASN143 4.3 29.1 1.0 N A:GLY144 4.4 29.9 1.0 CB A:HIS104 4.4 35.9 1.0 CA A:GLY144 4.4 31.7 1.0 CB A:ASN143 4.5 29.8 1.0 N A:LYS105 4.5 36.6 1.0 OD1 A:ASP136 4.5 30.9 1.0 CB A:ASN102 4.6 33.8 1.0 OD1 A:ASP195 4.6 31.1 1.0 CA A:ASN102 4.7 33.7 1.0 CA A:LYS105 4.7 36.5 1.0 C A:LYS105 4.9 35.6 1.0 C A:ASN102 4.9 34.4 1.0 N A:ASP136 4.9 37.4 1.0 CA A:ASP136 5.0 35.0 1.0

Calcium binding site 4 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:41.0 occ:1.00 OD2 B:ASP103 2.3 37.6 1.0 OD1 B:ASP67 2.3 39.6 1.0 OE1 B:GLU69 2.3 30.0 1.0 OE1 B:GLU11 2.4 36.6 1.0 CG B:ASP67 3.0 37.9 1.0 CG B:ASP103 3.3 37.0 1.0 CD B:GLU11 3.5 35.3 1.0 CD B:GLU69 3.6 32.6 1.0 OD2 B:ASP67 3.7 36.8 1.0 OD1 B:ASP103 3.7 36.9 1.0 OE2 B:GLU11 3.9 36.7 1.0 CB B:ASP67 3.9 36.9 1.0 CA B:ASP67 4.0 34.9 1.0 OD1 B:ASN12 4.1 39.2 1.0 ND2 B:ASN12 4.2 35.2 1.0 N B:ARG68 4.2 33.9 1.0 CB B:GLU69 4.4 34.3 1.0 N B:GLU69 4.4 36.5 1.0 C B:ASP67 4.4 34.0 1.0 CG B:GLU69 4.5 32.8 1.0 NE2 B:HIS104 4.5 40.7 1.0 OE2 B:GLU69 4.5 31.2 1.0 CA B:CA303 4.6 31.6 1.0 CG B:ASN12 4.6 35.3 1.0 CB B:ASP103 4.6 36.5 1.0 CG B:GLU11 4.7 33.9 1.0 CD2 B:HIS104 4.9 38.7 1.0

Calcium binding site 5 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:35.7 occ:1.00 OD1 B:ASN102 2.2 32.8 1.0 O B:ASN143 2.3 33.6 1.0 O B:HIS104 2.4 34.1 1.0 OD2 B:ASP136 2.5 39.0 1.0 OD1 B:ASP134 2.5 30.9 1.0 OD2 B:ASP134 2.5 31.2 1.0 OD2 B:ASP195 2.5 28.8 1.0 CG B:ASP134 2.8 31.1 1.0 CG B:ASN102 3.3 33.6 1.0 CG B:ASP195 3.4 28.3 1.0 C B:ASN143 3.4 32.3 1.0 CG B:ASP136 3.5 36.4 1.0 C B:HIS104 3.6 35.0 1.0 CB B:ASP195 3.7 27.9 1.0 CB B:ASP136 3.8 35.7 1.0 ND2 B:ASN102 3.9 34.1 1.0 O B:HOH401 4.0 32.1 1.0 CA B:ASN143 4.3 32.4 1.0 CB B:ASP134 4.3 31.8 1.0 N B:GLY144 4.3 31.4 1.0 CA B:HIS104 4.4 35.8 1.0 N B:HIS104 4.4 37.0 1.0 CA B:GLY144 4.4 32.4 1.0 CB B:ASN143 4.5 32.2 1.0 OD1 B:ASP195 4.5 28.8 1.0 CB B:HIS104 4.5 36.7 1.0 N B:LYS105 4.5 35.5 1.0 CB B:ASN102 4.6 33.5 1.0 OD1 B:ASP136 4.6 36.6 1.0 CA B:LYS105 4.7 35.5 1.0 CA B:ASN102 4.7 33.9 1.0 C B:LYS105 4.9 33.7 1.0 C B:ASN102 4.9 33.9 1.0 N B:ASP136 5.0 35.9 1.0

Calcium binding site 6 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:31.6 occ:1.00 OD1 B:ASP100 2.2 31.6 1.0 O B:GLN101 2.2 32.6 1.0 OD1 B:ASP103 2.3 36.9 1.0 OD1 B:ASP136 2.3 36.6 1.0 OE2 B:GLU11 2.3 36.7 1.0 OE2 B:GLU69 2.4 31.2 1.0 CD B:GLU69 3.1 32.6 1.0 OE1 B:GLU69 3.1 30.0 1.0 CG B:ASP100 3.2 33.7 1.0 CG B:ASP103 3.3 37.0 1.0 CG B:ASP136 3.4 36.4 1.0 C B:GLN101 3.4 33.9 1.0 CD B:GLU11 3.5 35.3 1.0 OD2 B:ASP100 3.7 33.6 1.0 N B:GLN101 3.7 34.0 1.0 OD2 B:ASP103 3.8 37.6 1.0 N B:ASP103 3.9 34.0 1.0 OE1 B:GLU11 3.9 36.6 1.0 CB B:ASP136 4.0 35.7 1.0 CA B:GLN101 4.1 34.4 1.0 CD2 B:HIS104 4.2 38.7 1.0 CA B:ASP136 4.2 36.2 1.0 OD2 B:ASP136 4.3 39.0 1.0 CB B:ASP100 4.4 34.3 1.0 CB B:ASP103 4.5 36.5 1.0 N B:ASN102 4.5 34.6 1.0 CG B:GLU69 4.5 32.8 1.0 NE B:ARG68 4.5 36.5 1.0 CA B:CA301 4.6 41.0 1.0 C B:ASP100 4.6 35.5 1.0 CA B:ASP100 4.6 34.5 1.0 CA B:ASP103 4.6 35.9 1.0 CA B:ASN102 4.7 33.9 1.0 CB B:GLN101 4.7 34.6 1.0 CG B:GLU11 4.7 33.9 1.0 NH2 B:ARG68 4.7 35.9 1.0 C B:ASN102 4.8 33.9 1.0

Calcium binding site 7 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:49.9 occ:1.00 OD1 C:ASP100 2.2 52.1 1.0 OD1 C:ASP103 2.3 46.4 1.0 OD1 C:ASP136 2.3 46.7 1.0 O C:GLN101 2.3 45.2 1.0 OE2 C:GLU69 2.3 48.1 1.0 OE2 C:GLU11 2.4 46.7 1.0 CD C:GLU69 3.0 50.0 1.0 OE1 C:GLU69 3.0 51.5 1.0 CG C:ASP100 3.3 51.0 1.0 CG C:ASP103 3.3 47.0 1.0 CG C:ASP136 3.3 45.5 1.0 C C:GLN101 3.5 48.4 1.0 CD C:GLU11 3.5 47.1 1.0 OD2 C:ASP100 3.7 50.2 1.0 N C:GLN101 3.8 51.3 1.0 OD2 C:ASP103 3.8 46.7 1.0 OE1 C:GLU11 3.9 48.3 1.0 N C:ASP103 3.9 49.2 1.0 CB C:ASP136 4.0 45.2 1.0 CD2 C:HIS104 4.1 49.9 1.0 CA C:ASP136 4.2 44.8 1.0 CA C:GLN101 4.2 51.2 1.0 OD2 C:ASP136 4.2 43.7 1.0 CG C:GLU69 4.4 49.0 1.0 CA C:CA303 4.4 60.6 1.0 CB C:ASP103 4.5 48.6 1.0 CB C:ASP100 4.5 50.4 1.0 N C:ASN102 4.5 48.3 1.0 NE C:ARG68 4.5 64.8 1.0 CA C:ASP103 4.6 49.4 1.0 CA C:ASP100 4.7 48.5 1.0 C C:ASP100 4.7 50.0 1.0 CA C:ASN102 4.7 48.2 1.0 NH2 C:ARG68 4.7 70.2 1.0 CG C:GLU11 4.8 47.0 1.0 CB C:GLN101 4.8 52.3 1.0 C C:ASN102 4.8 49.4 1.0 NE2 C:HIS104 4.9 51.0 1.0 N C:HIS104 5.0 49.2 1.0

Calcium binding site 8 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


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-Long) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:45.4 occ:1.00 OD1 C:ASN102 2.2 47.7 1.0 O C:HIS104 2.3 52.4 1.0 O C:ASN143 2.4 47.6 1.0 OD2 C:ASP195 2.4 50.5 1.0 OD2 C:ASP134 2.5 50.0 1.0 OD2 C:ASP136 2.5 43.7 1.0 OD1 C:ASP134 2.5 48.1 1.0 CG C:ASP134 2.9 48.3 1.0 CG C:ASP195 3.3 49.9 1.0 CG C:ASN102 3.4 47.8 1.0 CG C:ASP136 3.5 45.5 1.0 C C:ASN143 3.5 47.2 1.0 C C:HIS104 3.5 50.6 1.0 CB C:ASP195 3.6 47.2 1.0 CB C:ASP136 3.9 45.2 1.0 ND2 C:ASN102 3.9 49.2 1.0 CA C:HIS104 4.3 50.4 1.0 N C:HIS104 4.4 49.2 1.0 CB C:ASP134 4.4 46.3 1.0 CA C:ASN143 4.4 47.4 1.0 N C:GLY144 4.4 47.6 1.0 OD1 C:ASP195 4.4 53.2 1.0 N C:LYS105 4.5 50.8 1.0 CB C:HIS104 4.5 49.9 1.0 CA C:GLY144 4.5 46.9 1.0 CB C:ASN143 4.6 47.9 1.0 CB C:ASN102 4.6 48.2 1.0 CA C:LYS105 4.6 52.4 1.0 OD1 C:ASP136 4.6 46.7 1.0 CA C:ASN102 4.7 48.2 1.0 C C:LYS105 4.8 50.1 1.0 N C:PRO106 4.9 48.3 1.0 C C:ASN102 4.9 49.4 1.0 CD C:PRO106 5.0 47.9 1.0

Calcium binding site 9 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:60.6 occ:1.00 OE1 C:GLU69 2.3 51.5 1.0 OD2 C:ASP103 2.3 46.7 1.0 OD1 C:ASP67 2.3 54.9 1.0 OE1 C:GLU11 2.5 48.3 1.0 CG C:ASP67 3.1 54.7 1.0 CG C:ASP103 3.3 47.0 1.0 CD C:GLU11 3.5 47.1 1.0 CD C:GLU69 3.5 50.0 1.0 OD1 C:ASP103 3.6 46.4 1.0 OD2 C:ASP67 3.7 55.7 1.0 OE2 C:GLU11 3.9 46.7 1.0 CB C:ASP67 3.9 53.5 1.0 CA C:ASP67 4.1 52.1 1.0 OD1 C:ASN12 4.1 52.0 1.0 ND2 C:ASN12 4.2 52.3 1.0 N C:ARG68 4.2 53.4 1.0 CB C:GLU69 4.3 49.0 1.0 N C:GLU69 4.3 50.7 1.0 NE2 C:HIS104 4.3 51.0 1.0 CG C:GLU69 4.4 49.0 1.0 OE2 C:GLU69 4.4 48.1 1.0 C C:ASP67 4.4 52.9 1.0 CA C:CA301 4.4 49.9 1.0 CB C:ASP103 4.6 48.6 1.0 CG C:ASN12 4.6 51.8 1.0 CG C:GLU11 4.7 47.0 1.0 CD2 C:HIS104 4.8 49.9 1.0 CA C:GLU69 5.0 49.2 1.0

Calcium binding site 10 out of 18 in the Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human P-Cadherin (Ss-X-Dimer-Long) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:42.7 occ:1.00 O D:HIS104 2.2 53.3 1.0 OD1 D:ASP134 2.4 56.5 1.0 OD1 D:ASN102 2.4 51.8 1.0 OD2 D:ASP134 2.4 54.5 1.0 OD2 D:ASP136 2.5 53.6 1.0 O D:ASN143 2.5 47.4 1.0 OD2 D:ASP195 2.5 48.0 1.0 CG D:ASP134 2.7 56.3 1.0 C D:HIS104 3.4 54.0 1.0 CG D:ASP195 3.5 48.5 1.0 CG D:ASP136 3.5 54.8 1.0 CG D:ASN102 3.5 51.9 1.0 C D:ASN143 3.6 48.4 1.0 CB D:ASP195 3.7 49.0 1.0 CB D:ASP136 3.9 55.6 1.0 ND2 D:ASN102 4.1 53.2 1.0 CA D:HIS104 4.2 52.2 1.0 CB D:ASP134 4.2 57.7 1.0 N D:HIS104 4.3 52.4 1.0 CB D:HIS104 4.4 51.3 1.0 N D:LYS105 4.4 56.0 1.0 N D:GLY144 4.5 49.5 1.0 CA D:GLY144 4.5 49.9 1.0 CA D:LYS105 4.5 57.2 1.0 CA D:ASN143 4.5 49.0 1.0 OD1 D:ASP195 4.6 48.7 1.0 OD1 D:ASP136 4.6 56.6 1.0 C D:LYS105 4.7 56.1 1.0 CB D:ASN143 4.7 48.9 1.0 CB D:ASN102 4.8 51.7 1.0 CA D:ASN102 4.8 52.4 1.0 N D:PRO106 4.9 54.7 1.0 N D:ASP136 4.9 57.5 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