Calcium in PDB 3lnd: Crystal Structure of Cadherin-6 EC12 W4A

The structure of Crystal Structure of Cadherin-6 EC12 W4A, PDB code: 3lnd was solved by X.Jin, O.Harrison, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.979, 113.555, 67.907, 90.00, 96.01, 90.00
R / Rfree (%)	20.7 / 28.2

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Cadherin-6 EC12 W4A (pdb code 3lnd). 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 Cadherin-6 EC12 W4A, PDB code: 3lnd:
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 Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca208 b:43.4 occ:1.00 O A:ASN102 2.4 55.3 1.0 OD2 A:ASP134 2.4 59.4 1.0 O A:SER141 2.5 59.4 1.0 OD1 A:ASN100 2.5 55.9 1.0 OD2 A:ASP132 2.5 60.3 1.0 OD1 A:ASP187 2.7 62.6 1.0 OD2 A:ASP187 2.8 62.0 1.0 OD1 A:ASP132 2.8 60.2 1.0 CG A:ASP187 3.0 60.7 1.0 CG A:ASP132 3.1 59.8 1.0 CG A:ASP134 3.5 59.5 1.0 C A:ASN102 3.5 55.3 1.0 C A:SER141 3.7 59.6 1.0 CG A:ASN100 3.7 55.3 1.0 CB A:ASP134 4.0 59.6 1.0 N A:ASN102 4.1 54.8 1.0 CA A:ASN102 4.3 54.9 1.0 CB A:ASP187 4.4 60.0 1.0 ND2 A:ASN100 4.5 56.0 1.0 CB A:ASN102 4.5 54.8 1.0 OD1 A:ASP134 4.5 60.1 1.0 CB A:ASP132 4.6 59.1 1.0 CA A:SER141 4.6 59.5 1.0 N A:GLU103 4.6 55.9 1.0 N A:ALA142 4.6 59.8 1.0 CA A:ALA142 4.6 59.9 1.0 CD A:PRO104 4.7 56.5 1.0 CD1 A:LEU195 4.7 57.4 1.0 C A:GLU103 4.8 56.5 1.0 CB A:ASN100 4.8 54.6 1.0 N A:PRO104 4.8 56.4 1.0 CA A:GLU103 4.8 56.5 1.0 N A:ASP101 4.8 54.4 1.0 CA A:ASN100 4.8 54.5 1.0 CB A:SER141 4.9 59.6 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca209 b:51.3 occ:1.00 OE1 A:GLU11 2.4 61.3 1.0 OD1 A:ASP134 2.4 60.1 1.0 OD1 A:ASP98 2.5 54.4 1.0 OE2 A:GLU66 2.5 52.2 1.0 O A:ILE99 2.6 54.6 1.0 OD2 A:ASP101 2.6 53.0 1.0 OE1 A:GLU66 2.9 52.1 1.0 CD A:GLU66 3.0 52.3 1.0 CD A:GLU11 3.2 61.6 1.0 OE2 A:GLU11 3.3 60.1 1.0 CG A:ASP134 3.6 59.5 1.0 ND2 A:ASN102 3.6 54.8 1.0 CG A:ASP98 3.7 55.1 1.0 CG A:ASP101 3.7 53.7 1.0 C A:ILE99 3.8 54.7 1.0 CA A:CA210 3.8 54.7 1.0 N A:ILE99 4.1 54.8 1.0 CB A:ASP134 4.2 59.6 1.0 N A:ASP101 4.2 54.4 1.0 OD1 A:ASP101 4.2 52.0 1.0 CA A:ASP134 4.4 59.5 1.0 OD2 A:ASP98 4.4 55.9 1.0 NH1 A:ARG65 4.4 53.1 1.0 CG A:GLU66 4.4 52.8 1.0 CA A:ILE99 4.6 54.5 1.0 OD2 A:ASP134 4.6 59.4 1.0 CG1 A:ILE99 4.6 53.7 1.0 CG A:GLU11 4.7 61.9 1.0 CB A:ASP98 4.7 55.2 1.0 N A:ASN100 4.8 54.7 1.0 CB A:ASP101 4.8 54.4 1.0 CA A:ASP98 4.8 55.4 1.0 CB A:ARG65 4.9 53.8 1.0 CG A:ASN102 4.9 54.4 1.0 CA A:ASP101 4.9 54.4 1.0 C A:ASP98 4.9 55.1 1.0 CD A:ARG65 4.9 53.5 1.0 CA A:ASN100 5.0 54.5 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca210 b:54.7 occ:1.00 OE1 A:GLU66 2.4 52.1 1.0 OE2 A:GLU11 2.4 60.1 1.0 OD1 A:ASP64 2.5 55.2 1.0 OD1 A:ASP101 2.6 52.0 1.0 OE2 A:GLU12 2.8 63.8 1.0 OE1 A:GLU12 3.1 63.1 1.0 OD2 A:ASP101 3.2 53.0 1.0 CD A:GLU12 3.2 62.8 1.0 CG A:ASP101 3.3 53.7 1.0 CG A:ASP64 3.3 55.1 1.0 CD A:GLU11 3.5 61.6 1.0 CD A:GLU66 3.6 52.3 1.0 CA A:CA209 3.8 51.3 1.0 OE1 A:GLU11 4.0 61.3 1.0 OD2 A:ASP64 4.0 54.9 1.0 N A:ARG65 4.1 54.3 1.0 CB A:ASP64 4.1 55.1 1.0 CA A:ASP64 4.1 55.0 1.0 ND2 A:ASN102 4.3 54.8 1.0 N A:GLU66 4.4 53.7 1.0 C A:ASP64 4.4 54.8 1.0 OE2 A:GLU66 4.5 52.2 1.0 CG A:GLU12 4.5 61.9 1.0 CG A:GLU66 4.5 52.8 1.0 CB A:GLU66 4.6 53.4 1.0 CG A:GLU11 4.6 61.9 1.0 CB A:ASP101 4.7 54.4 1.0 CB A:GLU11 5.0 62.7 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca208 b:39.2 occ:1.00 OD1 B:ASN100 2.2 59.0 1.0 OD2 B:ASP134 2.3 56.0 1.0 O B:ASN102 2.4 58.3 1.0 OD1 B:ASP187 2.4 59.9 1.0 O B:SER141 2.4 59.0 1.0 OD1 B:ASP132 2.5 55.4 1.0 OD2 B:ASP132 2.6 55.5 1.0 CG B:ASP132 2.9 55.2 1.0 CG B:ASP187 3.3 58.3 1.0 CG B:ASP134 3.4 55.7 1.0 CG B:ASN100 3.4 59.5 1.0 C B:ASN102 3.5 58.4 1.0 C B:SER141 3.6 59.1 1.0 CB B:ASP134 3.8 55.5 1.0 CB B:ASP187 3.9 56.9 1.0 N B:ASN102 4.1 58.6 1.0 ND2 B:ASN100 4.1 60.6 1.0 OD2 B:ASP187 4.2 59.3 1.0 CA B:ASN102 4.2 58.5 1.0 CB B:ASP132 4.4 54.3 1.0 OD1 B:ASP134 4.5 55.2 1.0 CA B:SER141 4.5 59.2 1.0 CB B:ASN102 4.5 58.3 1.0 CB B:ASN100 4.6 59.0 1.0 N B:ALA142 4.6 59.2 1.0 N B:GLU103 4.6 58.4 1.0 CA B:ASN100 4.7 58.9 1.0 CD1 B:LEU195 4.7 56.2 1.0 CA B:ALA142 4.7 59.2 1.0 N B:ASP101 4.7 59.0 1.0 CB B:SER141 4.9 59.3 1.0 C B:ASN100 4.9 58.9 1.0 CB B:LEU195 4.9 57.3 1.0 N B:ASP134 4.9 55.2 1.0 CA B:GLU103 4.9 58.6 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca209 b:41.7 occ:1.00 O B:ILE99 2.3 57.9 1.0 OD1 B:ASP98 2.3 58.8 1.0 OD2 B:ASP101 2.3 60.3 1.0 OE1 B:GLU11 2.3 58.2 1.0 OE1 B:GLU66 2.4 55.3 1.0 OD1 B:ASP134 2.5 55.2 1.0 OE2 B:GLU66 2.7 54.9 1.0 CD B:GLU66 2.9 55.1 1.0 CG B:ASP98 3.3 58.3 1.0 CG B:ASP101 3.4 59.3 1.0 CD B:GLU11 3.4 58.2 1.0 C B:ILE99 3.5 58.2 1.0 CG B:ASP134 3.5 55.7 1.0 N B:ILE99 3.7 57.6 1.0 OD2 B:ASP98 3.8 59.4 1.0 OE2 B:GLU11 3.9 58.1 1.0 OD1 B:ASP101 3.9 59.7 1.0 CA B:CA210 4.0 45.6 1.0 ND2 B:ASN102 4.0 58.6 1.0 CB B:ASP134 4.1 55.5 1.0 N B:ASP101 4.1 59.0 1.0 CA B:ILE99 4.2 57.8 1.0 CA B:ASP134 4.3 55.3 1.0 CG B:GLU66 4.3 55.5 1.0 CB B:ASP98 4.4 58.0 1.0 OD2 B:ASP134 4.5 56.0 1.0 CA B:ASP98 4.5 57.8 1.0 CG1 B:ILE99 4.5 57.1 1.0 N B:ASN100 4.5 58.7 1.0 C B:ASP98 4.5 57.7 1.0 CB B:ASP101 4.6 58.9 1.0 CG B:GLU11 4.7 58.4 1.0 CA B:ASN100 4.7 58.9 1.0 CA B:ASP101 4.8 58.8 1.0 C B:ASN100 4.9 58.9 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca210 b:45.6 occ:1.00 OD2 B:ASP64 2.2 56.7 1.0 OE2 B:GLU66 2.2 54.9 1.0 OD1 B:ASP101 2.4 59.7 1.0 OE2 B:GLU11 2.6 58.1 1.0 OE2 B:GLU12 2.8 59.5 1.0 CG B:ASP64 3.2 56.9 1.0 CG B:ASP101 3.2 59.3 1.0 CD B:GLU11 3.2 58.2 1.0 OD2 B:ASP101 3.3 60.3 1.0 OE1 B:GLU11 3.4 58.2 1.0 CD B:GLU66 3.5 55.1 1.0 CD B:GLU12 3.8 59.5 1.0 OD1 B:ASP64 3.9 58.0 1.0 CA B:CA209 4.0 41.7 1.0 CG B:GLU12 4.1 59.2 1.0 CB B:GLU66 4.1 55.7 1.0 N B:GLU66 4.2 56.0 1.0 N B:ARG65 4.2 55.8 1.0 CB B:ASP64 4.2 56.2 1.0 CA B:ASP64 4.2 56.1 1.0 ND2 B:ASN102 4.2 58.6 1.0 CG B:GLU66 4.2 55.5 1.0 OE1 B:GLU66 4.4 55.3 1.0 C B:ASP64 4.4 55.8 1.0 CG B:GLU11 4.5 58.4 1.0 CB B:ASP101 4.6 58.9 1.0 CA B:GLU66 4.8 55.9 1.0 OE1 B:GLU12 4.9 59.8 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca208 b:39.1 occ:1.00 OD1 C:ASP132 2.3 59.1 1.0 O C:ASN102 2.3 57.9 1.0 OD1 C:ASN100 2.4 56.2 1.0 OD2 C:ASP132 2.5 59.5 1.0 OD1 C:ASP134 2.5 60.5 1.0 OD1 C:ASP187 2.7 62.4 1.0 O C:SER141 2.7 60.6 1.0 CG C:ASP132 2.7 58.8 1.0 OD2 C:ASP187 2.8 62.9 1.0 CG C:ASP187 3.0 61.3 1.0 CG C:ASP134 3.5 59.1 1.0 C C:ASN102 3.5 58.1 1.0 CG C:ASN100 3.6 56.1 1.0 C C:SER141 3.8 60.6 1.0 CB C:ASP134 3.9 58.7 1.0 N C:ASN102 4.1 57.1 1.0 CA C:ASN102 4.2 57.5 1.0 CB C:ASP132 4.3 58.4 1.0 ND2 C:ASN100 4.3 56.1 1.0 CB C:ASN102 4.4 57.4 1.0 CB C:ASP187 4.4 60.3 1.0 OD2 C:ASP134 4.6 58.5 1.0 N C:GLU103 4.6 58.8 1.0 CA C:SER141 4.6 60.5 1.0 N C:ALA142 4.6 60.8 1.0 CA C:ALA142 4.7 61.0 1.0 CB C:SER141 4.7 60.4 1.0 N C:ASP134 4.8 58.6 1.0 CB C:ASN100 4.8 55.9 1.0 CA C:ASN100 4.9 55.9 1.0 N C:ASP101 4.9 56.1 1.0 C C:GLU103 4.9 59.5 1.0 CD1 C:LEU195 4.9 57.5 1.0 CA C:GLU103 4.9 59.6 1.0 CA C:ASP134 5.0 58.7 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca209 b:48.7 occ:1.00 OE1 C:GLU11 2.3 61.3 1.0 O C:ILE99 2.4 55.0 1.0 OD2 C:ASP134 2.4 58.5 1.0 OD1 C:ASP98 2.5 55.4 1.0 OD2 C:ASP101 2.6 56.5 1.0 OE1 C:GLU66 2.6 51.8 1.0 OE2 C:GLU66 2.7 53.1 1.0 CD C:GLU66 3.0 52.8 1.0 CD C:GLU11 3.3 59.5 1.0 CG C:ASP134 3.4 59.1 1.0 C C:ILE99 3.6 55.2 1.0 CG C:ASP98 3.6 55.8 1.0 CG C:ASP101 3.6 55.6 1.0 OE2 C:GLU11 3.6 59.9 1.0 N C:ILE99 3.8 54.9 1.0 CB C:ASP134 4.0 58.7 1.0 OD1 C:ASP101 4.0 55.2 1.0 OD1 C:ASN102 4.1 56.4 1.0 CA C:ASP134 4.2 58.7 1.0 CA C:CA210 4.2 48.7 1.0 N C:ASP101 4.2 56.1 1.0 OD1 C:ASP134 4.3 60.5 1.0 OD2 C:ASP98 4.3 56.2 1.0 NH1 C:ARG65 4.4 54.4 1.0 CA C:ILE99 4.4 54.9 1.0 CG C:GLU66 4.4 53.2 1.0 CD C:ARG65 4.6 53.5 1.0 CB C:ASP98 4.6 55.3 1.0 N C:ASN100 4.6 55.5 1.0 CA C:ASP98 4.6 55.1 1.0 CG C:GLU11 4.6 59.7 1.0 CG1 C:ILE99 4.7 54.2 1.0 C C:ASP98 4.7 55.1 1.0 CA C:ASN100 4.8 55.9 1.0 CB C:ASP101 4.8 56.1 1.0 CB C:ARG65 4.8 54.1 1.0 C C:ASN100 5.0 56.1 1.0 CA C:ASP101 5.0 56.3 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca210 b:48.7 occ:1.00 OD1 C:ASP64 2.2 54.9 1.0 OE2 C:GLU11 2.3 59.9 1.0 OE2 C:GLU12 2.4 57.9 1.0 OE2 C:GLU66 2.4 53.1 1.0 OD1 C:ASP101 2.4 55.2 1.0 CG C:ASP64 3.2 55.0 1.0 CG C:ASP101 3.3 55.6 1.0 CD C:GLU12 3.3 58.8 1.0 OD2 C:ASP101 3.4 56.5 1.0 CD C:GLU11 3.4 59.5 1.0 CD C:GLU66 3.5 52.8 1.0 OE1 C:GLU12 3.7 58.9 1.0 OD2 C:ASP64 3.8 55.7 1.0 OE1 C:GLU11 3.9 61.3 1.0 CB C:ASP64 4.1 54.5 1.0 CA C:CA209 4.2 48.7 1.0 CA C:ASP64 4.2 54.3 1.0 N C:ARG65 4.3 54.2 1.0 CG C:GLU66 4.4 53.2 1.0 CB C:GLU66 4.4 53.9 1.0 OE1 C:GLU66 4.4 51.8 1.0 N C:GLU66 4.4 54.0 1.0 OD1 C:ASN102 4.4 56.4 1.0 CG C:GLU12 4.5 59.2 1.0 C C:ASP64 4.6 54.2 1.0 CG C:GLU11 4.6 59.7 1.0 CB C:ASP101 4.6 56.1 1.0 O C:HOH217 4.8 56.6 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Cadherin-6 EC12 W4A


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 Cadherin-6 EC12 W4A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca208 b:41.7 occ:1.00 OD1 D:ASP134 2.3 58.4 1.0 OD1 D:ASP132 2.3 56.1 1.0 O D:ASN102 2.3 57.0 1.0 OD1 D:ASN100 2.4 56.2 1.0 O D:SER141 2.4 58.0 1.0 OD1 D:ASP187 2.6 62.6 1.0 OD2 D:ASP187 2.7 62.6 1.0 CG D:ASP187 3.0 61.7 1.0 OD2 D:ASP132 3.0 56.1 1.0 CG D:ASP132 3.0 56.7 1.0 CG D:ASP134 3.4 57.7 1.0 C D:ASN102 3.5 57.1 1.0 CG D:ASN100 3.6 55.1 1.0 C D:SER141 3.6 58.1 1.0 CB D:ASP134 3.8 57.3 1.0 N D:ASN102 4.0 56.5 1.0 CA D:ASN102 4.2 56.9 1.0 ND2 D:ASN100 4.4 55.0 1.0 CB D:ASP187 4.4 61.4 1.0 OD2 D:ASP134 4.4 58.8 1.0 CB D:ASP132 4.5 56.9 1.0 CA D:SER141 4.5 58.2 1.0 N D:GLU103 4.6 57.5 1.0 N D:ALA142 4.6 57.9 1.0 CB D:ASN102 4.6 56.8 1.0 CD1 D:LEU195 4.7 59.4 1.0 CA D:ALA142 4.7 57.6 1.0 CB D:ASN100 4.7 54.8 1.0 N D:ASP101 4.7 55.5 1.0 CA D:ASN100 4.7 54.9 1.0 CB D:SER141 4.8 58.2 1.0 CA D:GLU103 4.8 57.8 1.0 CD D:PRO104 4.9 57.6 1.0 N D:ASP134 4.9 57.1 1.0 C D:ASN100 5.0 55.1 1.0

O.J.Harrison, F.Bahna, P.S.Katsamba, X.Jin, J.Brasch, J.Vendome, G.Ahlsen, K.J.Carroll, S.R.Price, B.Honig, L.Shapiro. Two-Step Adhesive Binding By Classical Cadherins. Nat.Struct.Mol.Biol. V. 17 348 2010.
ISSN: ISSN 1545-9993
PubMed: 20190754
DOI: 10.1038/NSMB.1784