Calcium in PDB 4num: Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M

The structure of Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M, PDB code: 4num was solved by X.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.751, 221.152, 72.239, 90.00, 103.85, 90.00
R / Rfree (%)	21.9 / 25.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M (pdb code 4num). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M, PDB code: 4num:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:51.2 occ:1.00 OD2 A:ASP136 2.1 59.0 1.0 OD2 A:ASP194 2.3 66.1 1.0 OD1 A:ASN102 2.3 72.2 1.0 O A:ASN104 2.4 59.5 1.0 OD2 A:ASP134 2.5 64.0 1.0 O A:ASN142 2.8 61.6 1.0 OD1 A:ASP134 3.1 65.0 1.0 CG A:ASP134 3.2 62.6 1.0 CG A:ASP136 3.4 60.7 1.0 CG A:ASP194 3.4 67.9 1.0 CG A:ASN102 3.5 70.1 1.0 C A:ASN104 3.6 63.4 1.0 CD1 A:LEU203 3.8 62.8 1.0 C A:ASN142 3.9 64.3 1.0 CB A:ASP194 4.0 69.2 1.0 CB A:ASP136 4.2 60.2 1.0 ND2 A:ASN102 4.2 70.5 1.0 OD1 A:ASP136 4.2 61.9 1.0 CA A:ARG105 4.3 64.0 1.0 OD1 A:ASP194 4.4 66.7 1.0 N A:ARG105 4.4 63.7 1.0 N A:ASN104 4.4 63.4 1.0 CA A:ASN142 4.5 66.8 1.0 CA A:ASN104 4.6 64.3 1.0 CB A:ASN142 4.6 66.7 1.0 CB A:ASP134 4.6 60.9 1.0 CA A:ASN102 4.6 66.7 1.0 CB A:ASN102 4.7 68.5 1.0 C A:ARG105 4.7 62.9 1.0 OD1 A:ASN104 4.7 69.1 1.0 CD A:PRO106 4.7 64.0 1.0 C A:ASN102 4.7 62.3 1.0 CB A:LEU203 4.9 62.6 1.0 CG A:LEU203 4.9 62.1 1.0 N A:GLY143 4.9 62.5 1.0 N A:PRO106 4.9 63.0 1.0 O A:ASN102 5.0 57.3 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:50.6 occ:1.00 OD1 A:ASP103 2.3 63.1 1.0 OE1 A:GLU11 2.4 66.0 1.0 OE2 A:GLU69 2.4 55.1 1.0 OD1 A:ASP100 2.5 60.4 1.0 O A:MET101 2.5 67.8 1.0 OD1 A:ASP136 2.6 61.9 1.0 CD A:GLU69 3.1 57.7 1.0 OE1 A:GLU69 3.1 55.5 1.0 CG A:ASP103 3.3 61.3 1.0 CD A:GLU11 3.4 66.7 1.0 CG A:ASP100 3.6 63.2 1.0 C A:MET101 3.7 68.9 1.0 CG A:ASP136 3.7 60.7 1.0 OE2 A:GLU11 3.8 65.6 1.0 OD2 A:ASP103 3.8 60.3 1.0 N A:MET101 3.9 67.6 1.0 OD1 A:ASN104 4.0 69.1 1.0 N A:ASP103 4.1 60.4 1.0 OD2 A:ASP100 4.2 63.5 1.0 CA A:ASP136 4.3 59.4 1.0 NE A:ARG68 4.4 79.9 1.0 CB A:ASP136 4.4 60.2 1.0 CA A:MET101 4.4 69.2 1.0 CB A:ASP103 4.4 60.6 1.0 CG A:GLU69 4.5 60.4 1.0 OD2 A:ASP136 4.7 59.0 1.0 CA A:CA303 4.7 72.0 1.0 N A:ASN102 4.7 67.8 1.0 CG A:GLU11 4.7 67.1 1.0 CA A:ASP103 4.7 60.6 1.0 C A:ASP100 4.8 65.7 1.0 CA A:ASP100 4.8 64.8 1.0 CB A:ASP100 4.8 64.9 1.0 CB A:ARG68 4.9 74.0 1.0 CG A:ASN104 4.9 66.0 1.0 CA A:ASN102 4.9 66.7 1.0 N A:ASP136 5.0 58.3 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:72.0 occ:1.00 OD1 A:ASP67 2.0 71.5 1.0 OD2 A:ASP103 2.1 60.3 1.0 OE1 A:GLU69 2.4 55.5 1.0 OE2 A:GLU11 2.6 65.6 1.0 CG A:ASP67 3.0 72.0 1.0 CG A:ASP103 3.3 61.3 1.0 CD A:GLU69 3.7 57.7 1.0 CD A:GLU11 3.7 66.7 1.0 ND2 A:ASN12 3.7 77.6 1.0 OD2 A:ASP67 3.7 72.0 1.0 OD1 A:ASP103 3.8 63.1 1.0 CB A:ASP67 3.9 72.8 1.0 CA A:ASP67 4.1 72.0 1.0 OD1 A:ASN12 4.2 80.4 1.0 OE1 A:GLU11 4.3 66.0 1.0 CG A:ASN12 4.4 77.3 1.0 CG A:GLU69 4.5 60.4 1.0 CB A:ASP103 4.5 60.6 1.0 CB A:GLU69 4.5 60.6 1.0 N A:ARG68 4.5 70.1 1.0 OE2 A:GLU69 4.6 55.1 1.0 C A:ASP67 4.6 70.6 1.0 CA A:CA302 4.7 50.6 1.0 N A:GLU69 4.7 66.3 1.0 CG A:GLU11 4.7 67.1 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:52.6 occ:1.00 OD2 B:ASP136 2.4 78.2 1.0 OD2 B:ASP134 2.4 75.5 1.0 O B:ASN142 2.5 68.7 1.0 OD1 B:ASN102 2.5 64.4 1.0 OD2 B:ASP194 2.5 70.9 1.0 O B:ASN104 2.7 62.4 1.0 OD1 B:ASP134 2.7 78.9 1.0 CG B:ASP134 2.9 78.1 1.0 CG B:ASP136 3.5 78.5 1.0 CG B:ASP194 3.6 71.7 1.0 CG B:ASN102 3.6 65.3 1.0 C B:ASN142 3.7 70.9 1.0 C B:ASN104 3.8 65.5 1.0 CB B:ASP194 3.9 72.0 1.0 CB B:ASP136 4.0 78.5 1.0 ND2 B:ASN102 4.1 65.1 1.0 CA B:ARG105 4.4 66.7 1.0 CB B:ASP134 4.4 79.6 1.0 C B:ARG105 4.5 65.7 1.0 N B:ARG105 4.5 67.0 1.0 OD1 B:ASP136 4.5 78.3 1.0 CA B:ASN142 4.6 73.1 1.0 CD1 B:LEU203 4.6 70.1 1.0 N B:GLY143 4.6 70.0 1.0 CD B:PRO106 4.6 66.4 1.0 OD1 B:ASP194 4.7 71.2 1.0 CA B:GLY143 4.7 71.0 1.0 N B:PRO106 4.7 65.8 1.0 N B:ASN104 4.8 65.7 1.0 CB B:ASN142 4.8 72.8 1.0 OD1 B:ASN104 4.8 65.0 1.0 CB B:ASN102 4.8 66.2 1.0 CA B:ASN104 4.9 66.3 1.0 CA B:ASN102 5.0 66.5 1.0 O B:ARG105 5.0 65.4 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:61.9 occ:1.00 OD1 B:ASP100 2.3 66.8 1.0 OD1 B:ASP136 2.3 78.3 1.0 O B:MET101 2.3 68.0 1.0 OE2 B:GLU69 2.3 50.4 1.0 OE1 B:GLU11 2.4 58.3 1.0 OD1 B:ASP103 2.6 69.3 1.0 CD B:GLU69 3.2 51.1 1.0 CG B:ASP103 3.3 67.2 1.0 CG B:ASP100 3.4 66.5 1.0 C B:MET101 3.5 68.6 1.0 CG B:ASP136 3.5 78.5 1.0 OE1 B:GLU69 3.5 49.2 1.0 CD B:GLU11 3.5 60.5 1.0 N B:MET101 3.7 66.6 1.0 OD2 B:ASP103 3.7 65.6 1.0 OD2 B:ASP100 4.0 66.2 1.0 OE2 B:GLU11 4.0 60.0 1.0 N B:ASP103 4.1 65.8 1.0 NE B:ARG68 4.1 61.2 1.0 CB B:ASP136 4.2 78.5 1.0 CA B:MET101 4.2 68.0 1.0 OD1 B:ASN104 4.3 65.0 1.0 CA B:ASP136 4.3 78.8 1.0 CB B:ASP103 4.4 66.8 1.0 OD2 B:ASP136 4.4 78.2 1.0 N B:ASN102 4.5 68.1 1.0 CB B:ASP100 4.6 66.9 1.0 CG B:GLU69 4.6 52.3 1.0 CA B:ASP100 4.6 66.5 1.0 C B:ASP100 4.6 65.5 1.0 CA B:ASN102 4.7 66.5 1.0 CG B:GLU11 4.7 61.5 1.0 CA B:ASP103 4.8 66.2 1.0 CD B:ARG68 4.8 61.5 1.0 CB B:MET101 4.9 67.5 1.0 CB B:ARG68 4.9 60.3 1.0 C B:ASN102 4.9 65.5 1.0 NH2 B:ARG68 4.9 64.9 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:70.9 occ:1.00 OD2 B:ASP103 2.2 65.6 1.0 OD1 B:ASP67 2.2 65.2 1.0 OE2 B:GLU11 2.8 60.0 1.0 OE1 B:GLU69 3.0 49.2 1.0 CG B:ASP67 3.1 64.7 1.0 ND2 B:ASN12 3.2 62.4 1.0 CG B:ASP103 3.4 67.2 1.0 CD B:GLU11 3.6 60.5 1.0 OD1 B:ASN12 3.7 62.9 1.0 CB B:ASP67 3.8 63.5 1.0 OD2 B:ASP67 3.8 65.7 1.0 CG B:ASN12 3.9 62.3 1.0 CA B:ASP67 4.0 61.3 1.0 OE1 B:GLU11 4.1 58.3 1.0 OD1 B:ASP103 4.2 69.3 1.0 CD B:GLU69 4.3 51.1 1.0 CB B:ASP103 4.3 66.8 1.0 CG B:GLU11 4.5 61.5 1.0 N B:ARG68 4.5 59.0 1.0 C B:ASP67 4.6 59.3 1.0 O B:LEU66 4.7 64.6 1.0 CB B:GLU11 4.9 62.1 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:65.1 occ:1.00 O C:ASN142 2.3 69.7 1.0 OD1 C:ASN102 2.4 70.4 1.0 OD2 C:ASP136 2.4 79.8 1.0 OD2 C:ASP194 2.5 75.1 1.0 OD2 C:ASP134 2.6 72.3 1.0 OD1 C:ASP134 2.8 75.9 1.0 O C:ASN104 3.0 67.2 1.0 CG C:ASP134 3.0 73.6 1.0 CG C:ASP194 3.4 74.2 1.0 C C:ASN142 3.4 75.2 1.0 CG C:ASP136 3.5 79.2 1.0 CG C:ASN102 3.6 70.9 1.0 CB C:ASP136 3.9 78.6 1.0 CB C:ASP194 3.9 73.2 1.0 C C:ASN104 4.0 71.6 1.0 CA C:ASN142 4.1 77.3 1.0 ND2 C:ASN102 4.2 72.3 1.0 CB C:ASN142 4.3 81.2 1.0 CD1 C:LEU203 4.4 70.8 1.0 OD1 C:ASP194 4.4 75.0 1.0 N C:GLY143 4.5 76.0 1.0 CB C:ASP134 4.5 74.2 1.0 OD1 C:ASP136 4.5 79.4 1.0 N C:ASN104 4.6 73.5 1.0 CA C:ASN102 4.6 70.9 1.0 OD1 C:ASN104 4.7 67.7 1.0 CB C:ASN102 4.7 70.3 1.0 CA C:ARG105 4.8 74.1 1.0 CA C:GLY143 4.8 76.9 1.0 N C:ARG105 4.8 74.0 1.0 C C:ASN102 4.9 69.9 1.0 CD C:PRO106 4.9 70.8 1.0 CA C:ASN104 4.9 72.0 1.0 C C:ARG105 4.9 73.0 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:61.0 occ:1.00 OD1 C:ASP136 2.2 79.4 1.0 OD1 C:ASP100 2.2 68.5 1.0 OE2 C:GLU69 2.3 61.2 1.0 OE1 C:GLU11 2.4 55.3 1.0 O C:MET101 2.6 71.3 1.0 OD1 C:ASP103 2.6 75.1 1.0 CD C:GLU69 3.2 63.2 1.0 CG C:ASP136 3.3 79.2 1.0 CG C:ASP100 3.4 70.0 1.0 OE1 C:GLU69 3.4 60.7 1.0 CD C:GLU11 3.5 56.1 1.0 CG C:ASP103 3.5 74.8 1.0 C C:MET101 3.7 74.0 1.0 N C:MET101 3.7 73.1 1.0 OE2 C:GLU11 3.9 55.1 1.0 OD2 C:ASP100 4.0 71.2 1.0 NE C:ARG68 4.0 74.5 1.0 CA C:ASP136 4.0 78.1 1.0 CB C:ASP136 4.0 78.6 1.0 OD2 C:ASP103 4.0 75.2 1.0 N C:ASP103 4.3 70.8 1.0 OD2 C:ASP136 4.3 79.8 1.0 CA C:MET101 4.4 74.9 1.0 OD1 C:ASN104 4.4 67.7 1.0 CB C:ASP100 4.5 70.3 1.0 CA C:ASP100 4.5 71.1 1.0 CG C:GLU69 4.6 64.9 1.0 C C:ASP100 4.6 71.5 1.0 CB C:ASP103 4.6 73.9 1.0 CD C:ARG68 4.6 72.2 1.0 CG C:GLU11 4.7 57.5 1.0 CB C:ARG68 4.8 66.8 1.0 CA C:CA303 4.8 73.4 1.0 NH2 C:ARG68 4.8 75.8 1.0 N C:ASP136 4.8 78.4 1.0 N C:ASN102 4.8 72.7 1.0 CZ C:ARG68 4.9 74.8 1.0 CA C:ASP103 4.9 72.8 1.0 N C:ASP137 5.0 78.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:73.4 occ:1.00 OD2 C:ASP103 2.0 75.2 1.0 OD1 C:ASP67 2.1 66.3 1.0 OE1 C:GLU69 2.3 60.7 1.0 OE2 C:GLU11 2.5 55.1 1.0 CG C:ASP67 3.1 67.4 1.0 CG C:ASP103 3.1 74.8 1.0 CD C:GLU11 3.3 56.1 1.0 CD C:GLU69 3.6 63.2 1.0 OD1 C:ASP103 3.7 75.1 1.0 ND2 C:ASN12 3.7 61.4 1.0 OE1 C:GLU11 3.8 55.3 1.0 CB C:ASP67 3.9 67.3 1.0 OD2 C:ASP67 3.9 69.4 1.0 CA C:ASP67 4.0 66.6 1.0 N C:ARG68 4.1 67.8 1.0 OD1 C:ASN12 4.1 63.4 1.0 CB C:ASP103 4.4 73.9 1.0 OE2 C:GLU69 4.4 61.2 1.0 C C:ASP67 4.4 67.0 1.0 CG C:ASN12 4.4 61.7 1.0 N C:GLU69 4.4 65.4 1.0 CG C:GLU11 4.4 57.5 1.0 CB C:GLU69 4.5 65.4 1.0 CG C:GLU69 4.5 64.9 1.0 CB C:GLU11 4.7 57.6 1.0 CA C:CA302 4.8 61.0 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Mouse N-Cadherin EC1-2 A78SI92M


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 Mouse N-Cadherin EC1-2 A78SI92M within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:44.6 occ:1.00 OD2 D:ASP136 2.2 62.8 1.0 OD1 D:ASN102 2.3 72.1 1.0 O D:ASN104 2.4 56.9 1.0 OD2 D:ASP194 2.4 63.4 1.0 OD2 D:ASP134 2.5 56.4 1.0 O D:ASN142 2.6 59.1 1.0 OD1 D:ASP134 2.9 60.5 1.0 CG D:ASP134 3.1 57.8 1.0 CG D:ASP136 3.4 61.7 1.0 CG D:ASP194 3.5 64.6 1.0 CG D:ASN102 3.5 69.2 1.0 C D:ASN104 3.6 61.6 1.0 C D:ASN142 3.8 64.5 1.0 CB D:ASP194 4.0 66.5 1.0 CB D:ASP136 4.0 60.8 1.0 ND2 D:ASN102 4.2 70.7 1.0 CD1 D:LEU203 4.2 64.4 1.0 OD1 D:ASN104 4.3 63.0 1.0 N D:ASN104 4.4 61.1 1.0 OD1 D:ASP136 4.4 61.1 1.0 CA D:ARG105 4.4 63.7 1.0 N D:ARG105 4.4 62.2 1.0 CA D:ASN142 4.5 67.4 1.0 OD1 D:ASP194 4.5 63.9 1.0 CA D:ASN102 4.6 64.7 1.0 CB D:ASP134 4.6 57.5 1.0 CA D:ASN104 4.6 63.1 1.0 CB D:ASN102 4.6 66.8 1.0 C D:ARG105 4.6 63.3 1.0 C D:ASN102 4.6 60.6 1.0 CB D:ASN142 4.7 67.8 1.0 CD D:PRO106 4.8 62.1 1.0 N D:GLY143 4.8 64.5 1.0 O D:ASN102 4.8 58.1 1.0 N D:PRO106 4.9 61.6 1.0 CA D:GLY143 4.9 65.5 1.0

J.Vendome, K.Felsovalyi, H.Song, Z.Yang, X.Jin, J.Brasch, O.J.Harrison, G.Ahlsen, F.Bahna, A.Kaczynska, P.S.Katsamba, D.Edmond, W.L.Hubbell, L.Shapiro, B.Honig. Structural and Energetic Determinants of Adhesive Binding Specificity in Type I Cadherins. Proc.Natl.Acad.Sci.Usa V. 111 E4175 2014.
ISSN: ISSN 0027-8424
PubMed: 25253890
DOI: 10.1073/PNAS.1416737111