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Calcium in PDB 4nup: Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3

Protein crystallography data

The structure of Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3, PDB code: 4nup was solved by X.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 175.504, 65.791, 102.505, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.9

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 4nup

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Calcium binding site 1 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:23.2
occ:1.00
 OD2 A:ASP103 2.2 15.2 1.0
OD1 A:ASP67 2.2 15.1 1.0
OE1 A:GLU69 2.3 13.5 1.0
O A:HOH437 2.4 11.6 1.0
OE1 A:GLU11 2.4 13.1 1.0
CG A:ASP103 3.1 13.8 1.0
CG A:ASP67 3.1 18.0 1.0
OD1 A:ASP103 3.4 10.6 1.0
CD A:GLU11 3.4 12.7 1.0
CD A:GLU69 3.4 12.7 1.0
OD2 A:ASP67 3.7 16.4 1.0
OE2 A:GLU11 3.8 9.2 1.0
O A:HOH512 3.9 14.9 1.0
CB A:GLU69 4.0 11.3 1.0
CG A:GLU69 4.0 15.7 1.0
CA A:CA302 4.1 9.3 1.0
O A:HOH469 4.1 13.3 1.0
ND2 A:ASN104 4.2 14.6 1.0
CB A:ASP67 4.2 14.9 1.0
N A:GLU69 4.3 13.1 1.0
CA A:ASP67 4.4 11.4 1.0
ND2 A:ASN12 4.4 15.0 1.0
O A:HOH523 4.4 18.6 1.0
N A:ARG68 4.4 14.8 1.0
OD1 A:ASN12 4.4 14.7 1.0
CB A:ASP103 4.5 8.7 1.0
OE2 A:GLU69 4.5 10.5 1.0
C A:ASP67 4.6 14.8 1.0
CG A:GLU11 4.7 10.7 1.0
CA A:GLU69 4.8 15.2 1.0
CG A:ASN12 4.8 12.9 1.0

Calcium binding site 2 out of 10 in 4nup

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Calcium binding site 2 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:9.3
occ:1.00
 OD1 A:ASP136 2.2 15.1 1.0
OD1 A:ASP100 2.3 15.5 1.0
OD1 A:ASP103 2.3 10.6 1.0
OE2 A:GLU11 2.4 9.2 1.0
O A:MET101 2.5 9.2 1.0
OE1 A:GLU69 2.5 13.5 1.0
OE2 A:GLU69 2.6 10.5 1.0
CD A:GLU69 2.8 12.7 1.0
CG A:ASP136 3.3 11.0 1.0
CG A:ASP103 3.4 13.8 1.0
CD A:GLU11 3.4 12.7 1.0
CG A:ASP100 3.4 16.0 1.0
C A:MET101 3.7 9.2 1.0
N A:MET101 3.7 9.9 1.0
ND2 A:ASN104 3.8 14.6 1.0
OE1 A:GLU11 3.8 13.1 1.0
OD2 A:ASP103 3.8 15.2 1.0
CB A:ASP136 3.9 11.6 1.0
OD2 A:ASP100 4.1 17.1 1.0
CA A:CA301 4.1 23.2 1.0
N A:ASP103 4.1 9.0 1.0
OD2 A:ASP136 4.1 13.2 1.0
CA A:ASP136 4.2 11.9 1.0
CG A:GLU69 4.3 15.7 1.0
CA A:MET101 4.3 9.0 1.0
NE A:ARG68 4.5 14.7 1.0
C A:ASP100 4.5 11.9 1.0
CA A:ASP100 4.5 10.4 1.0
CB A:ASP100 4.6 9.6 1.0
CB A:ASP103 4.6 8.7 1.0
N A:ASN102 4.7 10.5 1.0
CG A:GLU11 4.8 10.7 1.0
CA A:ASP103 4.8 8.1 1.0
CB A:ARG68 4.9 11.1 1.0
CA A:ASN102 4.9 9.2 1.0
CB A:MET101 4.9 8.8 1.0
CG A:ASN104 5.0 14.1 1.0
N A:ASP136 5.0 15.1 1.0
N A:ASN104 5.0 10.4 1.0
C A:ASP103 5.0 9.6 1.0

Calcium binding site 3 out of 10 in 4nup

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Calcium binding site 3 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:13.0
occ:1.00
 O A:ASN142 2.3 15.2 1.0
OD1 A:ASN102 2.3 12.4 1.0
O A:ASN104 2.3 12.8 1.0
OD2 A:ASP194 2.4 15.1 1.0
OD2 A:ASP136 2.4 13.2 1.0
OD2 A:ASP134 2.5 15.7 1.0
OD1 A:ASP134 2.6 14.0 1.0
CG A:ASP134 2.9 14.4 1.0
CG A:ASP194 3.4 13.1 1.0
C A:ASN142 3.4 14.5 1.0
CG A:ASN102 3.4 11.5 1.0
CG A:ASP136 3.5 11.0 1.0
C A:ASN104 3.5 11.4 1.0
CB A:ASP194 3.8 9.7 1.0
CB A:ASP136 3.9 11.6 1.0
ND2 A:ASN102 4.0 11.6 1.0
CA A:ASN142 4.2 12.4 1.0
CA A:ASN104 4.2 11.0 1.0
N A:ASN104 4.2 10.4 1.0
CB A:ASP134 4.3 11.4 1.0
CB A:ASN104 4.4 15.3 1.0
CB A:ASN142 4.4 12.4 1.0
N A:GLY143 4.4 10.9 1.0
OD1 A:ASP194 4.4 12.8 1.0
OD1 A:ASP136 4.6 15.1 1.0
N A:ARG105 4.6 10.0 1.0
CA A:GLY143 4.6 10.9 1.0
CB A:ASN102 4.7 7.2 1.0
CD1 A:LEU203 4.7 11.6 1.0
CA A:ASN102 4.7 9.2 1.0
CA A:ARG105 4.9 11.8 1.0
CD A:PRO106 4.9 17.0 1.0
C A:ARG105 5.0 15.4 1.0
N A:ASP136 5.0 15.1 1.0

Calcium binding site 4 out of 10 in 4nup

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Calcium binding site 4 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:18.0
occ:1.00
 OE1 B:GLU69 2.2 10.6 1.0
O B:HOH415 2.3 12.2 1.0
OD2 B:ASP103 2.4 13.7 1.0
OE1 B:GLU11 2.4 12.5 1.0
OD1 B:ASP67 2.4 17.1 1.0
O B:HOH408 2.4 10.2 1.0
CD B:GLU11 3.2 11.6 1.0
CG B:ASP103 3.2 11.1 1.0
CG B:ASP67 3.3 18.1 1.0
OD1 B:ASP103 3.3 8.6 1.0
CD B:GLU69 3.5 12.5 1.0
OE2 B:GLU11 3.5 7.9 1.0
CA B:CA302 3.8 9.7 1.0
OD2 B:ASP67 3.9 25.5 1.0
N B:ARG68 4.2 9.9 1.0
CA B:ASP67 4.2 7.8 1.0
OD1 B:ASN12 4.2 13.6 1.0
ND2 B:ASN12 4.2 10.1 1.0
CB B:ASP67 4.3 7.4 1.0
CG B:GLU69 4.3 8.7 1.0
N B:GLU69 4.3 15.5 1.0
CB B:GLU69 4.3 11.8 1.0
CG B:GLU11 4.4 8.4 1.0
OE2 B:GLU69 4.4 13.8 1.0
OD1 B:ASN104 4.5 10.1 1.0
O B:HOH418 4.5 8.8 1.0
O B:HOH577 4.5 19.6 1.0
C B:ASP67 4.5 11.7 1.0
CB B:ASP103 4.6 9.2 1.0
CG B:ASN12 4.7 10.5 1.0
CB B:GLU11 4.9 8.9 1.0
CA B:GLU69 5.0 15.5 1.0

Calcium binding site 5 out of 10 in 4nup

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Calcium binding site 5 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:9.7
occ:1.00
 OD1 B:ASP100 2.3 13.2 1.0
OD1 B:ASP103 2.4 8.6 1.0
OE2 B:GLU11 2.4 7.9 1.0
OD1 B:ASP136 2.4 10.7 1.0
O B:MET101 2.4 10.6 1.0
OE1 B:GLU69 2.7 10.6 1.0
OE2 B:GLU69 2.7 13.8 1.0
CD B:GLU69 3.0 12.5 1.0
CG B:ASP100 3.4 12.4 1.0
CD B:GLU11 3.4 11.6 1.0
CG B:ASP103 3.4 11.1 1.0
CG B:ASP136 3.5 12.5 1.0
C B:MET101 3.6 9.7 1.0
N B:MET101 3.7 8.3 1.0
OE1 B:GLU11 3.8 12.5 1.0
CA B:CA301 3.8 18.0 1.0
OD2 B:ASP103 3.9 13.7 1.0
OD2 B:ASP100 4.0 12.8 1.0
OD1 B:ASN104 4.1 10.1 1.0
CB B:ASP136 4.1 9.5 1.0
N B:ASP103 4.2 7.9 1.0
CA B:MET101 4.2 7.2 1.0
CA B:ASP136 4.3 8.8 1.0
NE B:ARG68 4.4 12.8 1.0
CG B:GLU69 4.4 8.7 1.0
OD2 B:ASP136 4.4 9.9 1.0
CA B:ASP100 4.5 9.8 1.0
C B:ASP100 4.5 8.7 1.0
CB B:ASP100 4.5 10.2 1.0
N B:ASN102 4.7 10.0 1.0
CB B:ASP103 4.7 9.2 1.0
CG B:GLU11 4.8 8.4 1.0
CB B:MET101 4.8 7.0 1.0
O B:HOH408 4.8 10.2 1.0
CB B:ARG68 4.8 10.8 1.0
CA B:ASP103 4.9 9.6 1.0
CA B:ASN102 4.9 8.3 1.0

Calcium binding site 6 out of 10 in 4nup

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Calcium binding site 6 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:8.3
occ:1.00
 OD1 B:ASN102 2.3 8.7 1.0
OD2 B:ASP136 2.3 9.9 1.0
O B:ASN104 2.3 14.4 1.0
O B:ASN142 2.4 9.7 1.0
OD2 B:ASP134 2.4 12.1 1.0
OD2 B:ASP194 2.5 10.0 1.0
OD1 B:ASP134 2.5 9.8 1.0
CG B:ASP134 2.7 12.0 1.0
CG B:ASP136 3.3 12.5 1.0
CG B:ASN102 3.5 9.9 1.0
CG B:ASP194 3.5 10.1 1.0
C B:ASN142 3.5 10.8 1.0
C B:ASN104 3.5 9.6 1.0
CB B:ASP136 3.7 9.5 1.0
CB B:ASP194 3.9 8.8 1.0
ND2 B:ASN102 4.1 7.6 1.0
CA B:ASN104 4.2 7.2 1.0
N B:ASN104 4.2 8.9 1.0
CB B:ASP134 4.2 9.9 1.0
CA B:ASN142 4.3 10.9 1.0
CB B:ASN104 4.4 8.6 1.0
OD1 B:ASP136 4.5 10.7 1.0
N B:GLY143 4.5 8.5 1.0
OD1 B:ASP194 4.5 9.0 1.0
N B:ARG105 4.5 11.1 1.0
CB B:ASN142 4.5 9.1 1.0
CA B:GLY143 4.6 7.8 1.0
CB B:ASN102 4.7 6.7 1.0
CA B:ASN102 4.7 8.3 1.0
CA B:ARG105 4.8 10.7 1.0
CD1 B:LEU203 4.8 7.5 1.0
N B:ASP136 4.8 7.4 1.0
CA B:ASP136 4.9 8.8 1.0
CD B:PRO106 4.9 14.5 1.0
C B:ARG105 4.9 16.2 1.0
C B:ASN102 5.0 8.2 1.0

Calcium binding site 7 out of 10 in 4nup

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Calcium binding site 7 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:32.9
occ:1.00
 OD1 C:ASP67 2.2 23.6 1.0
OD2 C:ASP103 2.2 17.4 1.0
OE1 C:GLU69 2.4 20.3 1.0
OE1 C:GLU11 2.4 16.9 1.0
CG C:ASP67 3.1 29.4 1.0
CG C:ASP103 3.2 16.6 1.0
O C:HOH482 3.3 22.8 1.0
CD C:GLU11 3.3 18.0 1.0
OD1 C:ASP103 3.6 16.6 1.0
CD C:GLU69 3.6 17.3 1.0
OD2 C:ASP67 3.7 33.2 1.0
OE2 C:GLU11 3.7 14.6 1.0
OD1 C:ASN12 4.0 19.6 1.0
O C:HOH559 4.0 34.9 1.0
CB C:ASP67 4.1 26.4 1.0
CA C:ASP67 4.2 17.2 1.0
CA C:CA302 4.2 13.8 1.0
N C:ARG68 4.3 19.4 1.0
CG C:GLU69 4.3 15.3 1.0
CB C:GLU69 4.3 20.8 1.0
ND2 C:ASN104 4.4 17.2 1.0
ND2 C:ASN12 4.4 12.4 1.0
N C:GLU69 4.4 21.6 1.0
CG C:GLU11 4.4 11.7 1.0
CB C:ASP103 4.5 19.6 1.0
C C:ASP67 4.5 21.3 1.0
OE2 C:GLU69 4.5 13.2 1.0
CG C:ASN12 4.6 14.7 1.0
CB C:GLU11 4.9 12.6 1.0

Calcium binding site 8 out of 10 in 4nup

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Calcium binding site 8 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:13.8
occ:1.00
 OD1 C:ASP103 2.3 16.6 1.0
OD1 C:ASP100 2.3 19.5 1.0
O C:MET101 2.3 18.4 1.0
OE2 C:GLU11 2.4 14.6 1.0
OE2 C:GLU69 2.5 13.2 1.0
OD1 C:ASP136 2.6 20.8 1.0
OE1 C:GLU69 2.7 20.3 1.0
CD C:GLU69 2.9 17.3 1.0
CG C:ASP103 3.3 16.6 1.0
CG C:ASP100 3.4 16.4 1.0
CD C:GLU11 3.4 18.0 1.0
CG C:ASP136 3.5 19.2 1.0
C C:MET101 3.5 19.7 1.0
N C:MET101 3.7 19.1 1.0
OD2 C:ASP103 3.7 17.4 1.0
OE1 C:GLU11 3.8 16.9 1.0
OD2 C:ASP100 3.9 18.5 1.0
ND2 C:ASN104 4.0 17.2 1.0
CB C:ASP136 4.0 17.6 1.0
N C:ASP103 4.1 16.5 1.0
CA C:MET101 4.1 18.6 1.0
CA C:CA301 4.2 32.9 1.0
CG C:GLU69 4.3 15.3 1.0
OD2 C:ASP136 4.3 19.9 1.0
CA C:ASP136 4.3 18.3 1.0
NE C:ARG68 4.4 23.7 1.0
C C:ASP100 4.5 21.2 1.0
CB C:ASP103 4.5 19.6 1.0
CA C:ASP100 4.6 15.5 1.0
CB C:ASP100 4.6 15.4 1.0
N C:ASN102 4.6 21.6 1.0
CB C:ARG68 4.7 15.0 1.0
CB C:MET101 4.7 18.3 1.0
CG C:GLU11 4.8 11.7 1.0
CA C:ASP103 4.8 19.7 1.0
CA C:ASN102 4.8 15.1 1.0
C C:ASN102 5.0 18.7 1.0

Calcium binding site 9 out of 10 in 4nup

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Calcium binding site 9 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:14.4
occ:1.00
 O C:ASN104 2.3 15.2 1.0
OD2 C:ASP136 2.3 19.9 1.0
OD2 C:ASP134 2.4 20.4 1.0
O C:ASN142 2.4 21.1 1.0
OD1 C:ASN102 2.4 19.4 1.0
OD1 C:ASP134 2.5 18.5 1.0
OD2 C:ASP194 2.5 14.3 1.0
CG C:ASP134 2.8 18.6 1.0
CG C:ASP136 3.4 19.2 1.0
CG C:ASP194 3.5 15.0 1.0
C C:ASN104 3.5 17.5 1.0
C C:ASN142 3.5 22.6 1.0
CG C:ASN102 3.5 20.9 1.0
CB C:ASP194 3.8 15.1 1.0
CB C:ASP136 3.8 17.6 1.0
ND2 C:ASN102 4.2 19.0 1.0
CA C:ASN104 4.2 18.9 1.0
CA C:ASN142 4.3 21.3 1.0
N C:ASN104 4.3 19.5 1.0
CB C:ASP134 4.3 16.9 1.0
CB C:ASN104 4.4 17.6 1.0
OD1 C:ASP136 4.5 20.8 1.0
OD1 C:ASP194 4.5 14.6 1.0
N C:ARG105 4.5 22.0 1.0
CB C:ASN142 4.5 20.8 1.0
N C:GLY143 4.6 16.8 1.0
CD1 C:LEU203 4.7 12.8 1.0
CA C:GLY143 4.7 22.3 1.0
CB C:ASN102 4.7 16.4 1.0
CA C:ASN102 4.8 15.1 1.0
CA C:ARG105 4.8 18.6 1.0
CD C:PRO106 4.9 16.1 1.0
N C:ASP136 4.9 15.2 1.0
C C:ARG105 4.9 15.4 1.0

Calcium binding site 10 out of 10 in 4nup

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Calcium binding site 10 out of 10 in the Crystal Structure of Mouse N-Cadherin EC1-2 with Aa Insertion Between Residues 2 and 3


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 with Aa Insertion Between Residues 2 and 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:34.1
occ:1.00
 OE1 C:GLU119 2.3 15.5 1.0
O C:HOH506 2.3 25.7 1.0
OD1 C:ASP215 2.5 25.0 1.0
O C:HOH459 2.5 26.1 1.0
CD C:GLU119 3.3 18.0 1.0
O C:HOH537 3.5 14.9 1.0
CG C:ASP215 3.5 24.8 1.0
OE2 C:GLU119 3.7 19.2 1.0
OD2 C:ASP215 3.9 29.7 1.0
O C:HOH512 4.2 14.2 1.0
O C:HOH457 4.4 22.6 1.0
CG C:GLU119 4.7 18.2 1.0
CB C:ASP215 4.9 14.7 1.0
O C:ASP215 4.9 16.3 1.0

Reference:

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
Page generated: Sat Dec 12 05:01:26 2020

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