Calcium in PDB 7cym: Crystal Structure of Li-Cadherin EC1-4

The structure of Crystal Structure of Li-Cadherin EC1-4, PDB code: 7cym was solved by J.M.M.Caaveiro, A.Yui, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.25 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.36, 70.84, 134.219, 90, 98.69, 90
R / Rfree (%)	22.2 / 27.4

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Li-Cadherin EC1-4 (pdb code 7cym). 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 Li-Cadherin EC1-4, PDB code: 7cym:
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 Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:66.8 occ:1.00 OD2 A:ASP154 2.2 79.1 1.0 O A:ASN122 2.3 55.8 1.0 OD1 A:ASN120 2.3 60.7 1.0 O A:ASN160 2.3 65.9 1.0 OD2 A:ASP152 2.4 65.9 1.0 OD1 A:ASP152 2.5 72.7 1.0 OD2 A:ASP215 2.5 66.7 1.0 CG A:ASP152 2.7 68.7 1.0 CG A:ASP154 3.3 73.0 1.0 CG A:ASP215 3.4 65.7 1.0 C A:ASN122 3.5 60.4 1.0 CG A:ASN120 3.6 61.2 1.0 C A:ASN160 3.6 68.1 1.0 CB A:ASP215 3.7 66.0 1.0 CB A:ASP154 4.0 72.0 1.0 CB A:ASP152 4.2 67.6 1.0 OD1 A:ASP154 4.3 74.0 1.0 ND2 A:ASN120 4.3 59.1 1.0 CA A:ASN122 4.3 62.4 1.0 N A:ASN122 4.4 62.6 1.0 CA A:ASN160 4.5 68.5 1.0 N A:GLY161 4.5 67.2 1.0 CB A:ASN122 4.5 63.1 1.0 N A:ARG123 4.5 62.5 1.0 OD1 A:ASP215 4.5 66.4 1.0 CB A:ASN120 4.6 62.9 1.0 CA A:GLY161 4.6 66.6 1.0 CD A:PRO124 4.7 63.1 1.0 CA A:ASN120 4.7 62.6 1.0 CA A:ARG123 4.8 64.1 1.0 C A:ARG123 4.8 63.0 1.0 CB A:ASN160 4.8 69.5 1.0 N A:PRO124 4.8 62.7 1.0 CD2 A:PHE224 4.8 63.6 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:67.1 occ:1.00 OE2 A:GLU87 2.1 62.4 1.0 O A:ILE119 2.2 58.7 1.0 OD1 A:ASP118 2.3 64.3 1.0 OD1 A:ASP121 2.4 65.0 1.0 OE2 A:GLU40 2.5 79.3 1.0 OD1 A:ASP154 2.5 74.0 1.0 CD A:GLU87 2.9 66.8 1.0 OE1 A:GLU87 3.0 67.0 1.0 CG A:ASP118 3.3 66.8 1.0 CG A:ASP121 3.4 66.5 1.0 C A:ILE119 3.4 61.6 1.0 CG A:ASP154 3.4 73.0 1.0 CD A:GLU40 3.4 73.3 1.0 OE1 A:GLU40 3.7 71.8 1.0 OD2 A:ASP118 3.7 71.0 1.0 N A:ILE119 3.8 62.8 1.0 ND2 A:ASN122 3.9 62.7 1.0 OD2 A:ASP121 3.9 71.7 1.0 CB A:ASP154 3.9 72.0 1.0 N A:ASP121 4.1 62.1 1.0 CA A:ASP154 4.2 71.5 1.0 CA A:CA505 4.2 70.8 1.0 CA A:ILE119 4.3 62.0 1.0 CG A:GLU87 4.3 67.7 1.0 OD2 A:ASP154 4.4 79.1 1.0 N A:ASN120 4.4 63.7 1.0 NH2 A:ARG86 4.5 64.7 1.0 CB A:ASP118 4.5 65.7 1.0 NE A:ARG86 4.5 67.0 1.0 CB A:ASP121 4.6 64.9 1.0 CA A:ASP118 4.6 65.7 1.0 CA A:ASN120 4.7 62.6 1.0 CG1 A:ILE119 4.7 63.2 1.0 C A:ASP118 4.7 64.5 1.0 CG A:GLU40 4.8 72.0 1.0 CA A:ASP121 4.8 64.0 1.0 CB A:ARG86 4.9 69.3 1.0 C A:ASN120 5.0 62.3 1.0 N A:ASN122 5.0 62.6 1.0 N A:ASP154 5.0 70.0 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:70.8 occ:1.00 OE1 A:GLU87 2.2 67.0 1.0 OD2 A:ASP121 2.2 71.7 1.0 OD1 A:ASP85 2.3 72.9 1.0 OE1 A:GLU40 2.5 71.8 1.0 CG A:ASP121 2.9 66.5 1.0 OD1 A:ASP121 3.2 65.0 1.0 CG A:ASP85 3.3 68.8 1.0 CD A:GLU87 3.4 66.8 1.0 CD A:GLU40 3.5 73.3 1.0 OE2 A:GLU40 3.9 79.3 1.0 OD2 A:ASP85 3.9 68.7 1.0 ND2 A:ASN122 4.1 62.7 1.0 CA A:CA504 4.2 67.1 1.0 CB A:GLU87 4.2 69.2 1.0 CG A:GLU87 4.2 67.7 1.0 CB A:ASP85 4.2 66.7 1.0 CB A:ASP121 4.2 64.9 1.0 OE2 A:GLU87 4.3 62.4 1.0 CA A:ASP85 4.4 67.2 1.0 N A:GLU87 4.5 68.8 1.0 N A:ARG86 4.6 69.7 1.0 C A:ASP85 4.8 68.9 1.0 CG A:GLU40 4.8 72.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:84.7 occ:1.00 OD1 A:ASP335 1.8 87.6 1.0 OD1 A:ASP299 2.1 76.6 1.0 OE1 A:GLU301 2.3 79.3 1.0 O7 C:NAG1 2.4 102.4 1.0 CG A:ASP335 2.7 86.3 1.0 OE1 A:GLU249 2.8 80.7 1.0 OD2 A:ASP335 3.1 85.5 1.0 CG A:ASP299 3.2 81.4 1.0 C7 C:NAG1 3.5 98.6 1.0 CD A:GLU249 3.5 79.0 1.0 CD A:GLU301 3.6 77.6 1.0 CB A:ASP299 3.8 83.3 1.0 OE2 A:GLU249 3.9 85.0 1.0 CB A:ASP335 4.0 85.2 1.0 CA A:ASP299 4.1 80.2 1.0 C2 C:NAG1 4.1 95.9 1.0 OD2 A:ASP299 4.1 85.4 1.0 CA A:CA507 4.2 72.7 1.0 N2 C:NAG1 4.2 97.9 1.0 ND2 A:ASN250 4.4 90.0 1.0 OE2 A:GLU301 4.5 77.3 1.0 N A:ARG300 4.5 73.6 1.0 C8 C:NAG1 4.5 100.8 1.0 CG A:GLU249 4.5 77.5 1.0 CG A:GLU301 4.6 78.7 1.0 CB A:GLU301 4.6 83.2 1.0 C A:ASP299 4.7 77.3 1.0 N A:GLU301 4.7 79.6 1.0 O3 C:NAG1 4.9 96.8 1.0 C1 C:NAG1 4.9 94.2 1.0 CB A:GLU249 5.0 78.6 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:72.7 occ:1.00 OE2 A:GLU301 2.1 77.3 1.0 OD2 A:ASP335 2.1 85.5 1.0 OD1 A:ASP332 2.3 70.7 1.0 O A:ILE333 2.3 66.8 1.0 CD A:GLU301 2.6 77.6 1.0 OE1 A:GLU301 2.7 79.3 1.0 OE2 A:GLU249 2.8 85.0 1.0 OD1 A:ASP368 2.9 94.9 1.0 CG A:ASP368 3.1 87.0 1.0 CG A:ASP335 3.4 86.3 1.0 CG A:ASP332 3.4 73.4 1.0 C A:ILE333 3.6 73.3 1.0 CB A:ASP368 3.6 81.9 1.0 OD2 A:ASP368 3.7 89.9 1.0 CD A:GLU249 3.8 79.0 1.0 CA A:ASP368 3.8 79.3 1.0 OE1 A:GLU249 4.0 80.7 1.0 N A:ASP335 4.0 80.5 1.0 OD2 A:ASP332 4.0 71.2 1.0 OD1 A:ASP335 4.0 87.6 1.0 N A:ILE333 4.0 76.5 1.0 CG A:GLU301 4.1 78.7 1.0 CA A:CA506 4.2 84.7 1.0 CA A:ILE333 4.4 75.8 1.0 CB A:ASP335 4.5 85.2 1.0 N A:ASN334 4.5 75.6 1.0 CB A:ASP332 4.6 74.8 1.0 NE A:ARG300 4.6 76.2 1.0 CA A:ASP335 4.7 83.1 1.0 CA A:ASN334 4.7 77.0 1.0 N A:ASP368 4.7 78.8 1.0 CA A:ASP332 4.7 75.4 1.0 N A:ASN336 4.8 86.0 1.0 C A:ASN334 4.8 78.4 1.0 CB A:ARG300 4.8 70.9 1.0 C A:ASP332 4.9 75.1 1.0 C A:ASP368 4.9 78.2 1.0 N A:GLU369 5.0 76.9 1.0 C A:ASP335 5.0 85.8 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca508 b:75.4 occ:1.00 O A:ASN336 2.3 83.6 1.0 OD1 A:ASN334 2.3 70.5 1.0 O A:ASN374 2.3 76.4 1.0 OD1 A:ASP366 2.4 74.5 1.0 OD2 A:ASP426 2.4 73.1 1.0 OD2 A:ASP366 2.4 68.2 1.0 CG A:ASP366 2.7 75.1 1.0 OD2 A:ASP368 2.8 89.9 1.0 CG A:ASP368 3.4 87.0 1.0 C A:ASN336 3.5 85.1 1.0 CG A:ASN334 3.5 75.3 1.0 CG A:ASP426 3.6 73.1 1.0 C A:ASN374 3.6 71.8 1.0 CB A:ASP368 3.9 81.9 1.0 OD1 A:ASP368 4.2 94.9 1.0 ND2 A:ASN334 4.2 74.8 1.0 CB A:ASP426 4.3 74.3 1.0 CB A:ASP366 4.3 76.9 1.0 N A:ASN336 4.4 86.0 1.0 CA A:ASN336 4.4 85.8 1.0 CA A:ASN374 4.4 73.9 1.0 N A:PRO337 4.4 87.6 1.0 CA A:PRO337 4.5 86.3 1.0 N A:SER375 4.5 68.6 1.0 OD1 A:ASP426 4.5 73.3 1.0 CA A:SER375 4.6 68.5 1.0 CD2 A:PHE429 4.6 80.8 1.0 CB A:ASN334 4.7 75.3 1.0 CA A:ASN334 4.7 77.0 1.0 C A:PRO337 4.8 85.1 1.0 CB A:ASN336 4.8 85.6 1.0 CB A:ASN374 4.8 73.5 1.0 N A:ASP368 4.9 78.8 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:66.6 occ:1.00 O B:ILE119 2.2 59.9 1.0 OE2 B:GLU87 2.2 57.7 1.0 OD1 B:ASP121 2.2 68.8 1.0 OD1 B:ASP118 2.4 63.2 1.0 OE2 B:GLU40 2.4 73.6 1.0 CD B:GLU87 2.9 66.2 1.0 OE1 B:GLU87 2.9 74.2 1.0 CG B:ASP121 3.2 71.8 1.0 CD B:GLU40 3.4 66.8 1.0 CG B:ASP118 3.4 69.2 1.0 C B:ILE119 3.4 65.0 1.0 OD1 B:ASP154 3.4 72.5 1.0 CG B:ASP154 3.5 70.3 1.0 OE1 B:GLU40 3.6 62.8 1.0 OD2 B:ASP121 3.7 65.4 1.0 OD2 B:ASP154 3.8 73.0 1.0 N B:ILE119 3.8 65.2 1.0 OD2 B:ASP118 3.8 73.0 1.0 ND2 B:ASN122 4.0 73.7 1.0 CB B:ASP154 4.0 69.7 1.0 N B:ASP121 4.1 68.6 1.0 CA B:ILE119 4.2 67.6 1.0 CA B:ASP154 4.3 69.1 1.0 CA B:CA503 4.3 72.8 1.0 CG B:GLU87 4.3 67.4 1.0 N B:ASN120 4.4 65.7 1.0 CB B:ASP121 4.5 72.2 1.0 CG1 B:ILE119 4.6 70.5 1.0 CB B:ASP118 4.6 69.5 1.0 NH2 B:ARG86 4.6 77.4 1.0 NE B:ARG86 4.6 79.7 1.0 CG B:GLU40 4.7 67.1 1.0 CA B:ASN120 4.7 67.7 1.0 CA B:ASP118 4.7 66.2 1.0 CA B:ASP121 4.7 73.4 1.0 C B:ASP118 4.7 64.9 1.0 N B:ASN122 5.0 76.3 1.0 C B:ASN120 5.0 67.5 1.0 CB B:ARG86 5.0 76.9 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:72.8 occ:1.00 OD1 B:ASP85 2.3 80.5 1.0 OD2 B:ASP121 2.3 65.4 1.0 OE1 B:GLU87 2.3 74.2 1.0 OE1 B:GLU40 2.4 62.8 1.0 O B:HOH621 2.5 65.0 1.0 CG B:ASP121 3.1 71.8 1.0 CG B:ASP85 3.2 77.9 1.0 CD B:GLU40 3.5 66.8 1.0 OD1 B:ASP121 3.5 68.8 1.0 CD B:GLU87 3.6 66.2 1.0 OD2 B:ASP85 3.9 81.2 1.0 OE2 B:GLU40 3.9 73.6 1.0 CB B:ASP85 4.0 74.2 1.0 CA B:ASP85 4.3 72.7 1.0 CA B:CA502 4.3 66.6 1.0 CB B:GLU87 4.4 69.3 1.0 CG B:GLU87 4.4 67.4 1.0 OE2 B:GLU87 4.4 57.7 1.0 CB B:ASP121 4.4 72.2 1.0 ND2 B:ASN122 4.4 73.7 1.0 N B:ARG86 4.6 71.3 1.0 N B:GLU87 4.6 71.5 1.0 C B:ASP85 4.7 70.6 1.0 CG B:GLU40 4.7 67.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:69.2 occ:1.00 O B:ASN122 2.2 74.7 1.0 O B:ASN160 2.3 70.4 1.0 OD1 B:ASN120 2.4 67.9 1.0 OD2 B:ASP152 2.4 66.6 1.0 OD1 B:ASP152 2.4 78.1 1.0 OD2 B:ASP215 2.6 68.1 1.0 CG B:ASP152 2.7 71.3 1.0 OD2 B:ASP154 2.8 73.0 1.0 CG B:ASP154 3.3 70.3 1.0 C B:ASN122 3.5 78.0 1.0 CG B:ASP215 3.5 67.7 1.0 C B:ASN160 3.5 72.2 1.0 CG B:ASN120 3.6 68.7 1.0 CB B:ASP215 3.8 70.2 1.0 OD1 B:ASP154 3.8 72.5 1.0 CB B:ASP154 3.9 69.7 1.0 CB B:ASP152 4.2 69.0 1.0 CA B:ASN122 4.3 77.5 1.0 N B:ASN122 4.3 76.3 1.0 CB B:ASN122 4.4 76.8 1.0 ND2 B:ASN120 4.4 68.1 1.0 CA B:ASN160 4.4 74.3 1.0 N B:GLY161 4.5 71.6 1.0 N B:ARG123 4.5 77.0 1.0 CA B:GLY161 4.5 71.7 1.0 CB B:ASN120 4.6 68.1 1.0 OD1 B:ASP215 4.7 66.7 1.0 CA B:ASN120 4.7 67.7 1.0 CB B:ASN160 4.7 75.7 1.0 C B:ARG123 4.8 70.7 1.0 CD B:PRO124 4.8 64.2 1.0 CA B:ARG123 4.8 74.8 1.0 N B:PRO124 4.8 65.1 1.0 CD2 B:PHE224 4.9 75.5 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Li-Cadherin EC1-4


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 Li-Cadherin EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:59.3 occ:1.00 OD2 B:ASP335 2.1 69.5 1.0 OE2 B:GLU301 2.1 64.5 1.0 OD1 B:ASP332 2.3 63.8 1.0 O B:ILE333 2.4 57.2 1.0 OE1 B:GLU301 2.6 68.2 1.0 OE2 B:GLU249 2.6 68.5 1.0 CD B:GLU301 2.6 65.8 1.0 OD1 B:ASP368 3.1 71.5 1.0 CG B:ASP335 3.2 66.3 1.0 CG B:ASP368 3.4 65.0 1.0 CG B:ASP332 3.5 63.1 1.0 CD B:GLU249 3.5 66.6 1.0 C B:ILE333 3.6 60.4 1.0 OE1 B:GLU249 3.7 67.4 1.0 OD1 B:ASP335 3.8 71.2 1.0 CA B:CA506 3.8 68.6 1.0 CB B:ASP368 3.9 63.6 1.0 OD2 B:ASP368 4.0 65.3 1.0 N B:ILE333 4.0 59.6 1.0 CA B:ASP368 4.1 61.9 1.0 N B:ASP335 4.1 59.9 1.0 OD2 B:ASP332 4.1 65.7 1.0 CG B:GLU301 4.1 65.8 1.0 ND2 B:ASN336 4.2 63.8 1.0 CB B:ASP335 4.4 64.3 1.0 CA B:ILE333 4.5 60.6 1.0 CB B:ASP332 4.6 64.2 1.0 NE B:ARG300 4.6 66.6 1.0 CA B:ASP332 4.6 64.4 1.0 N B:ASN334 4.6 59.6 1.0 CA B:ASP335 4.7 64.0 1.0 CB B:ARG300 4.7 61.2 1.0 C B:ASP332 4.8 62.1 1.0 CG1 B:ILE333 4.8 60.6 1.0 CA B:ASN334 4.8 58.9 1.0 CG B:GLU249 4.9 65.0 1.0 C B:ASN334 4.9 57.7 1.0 N B:ASN336 5.0 65.1 1.0 N B:ASP368 5.0 59.3 1.0

A.Yui, J.M.M.Caaveiro, D.Kuroda, M.Nakakido, S.Nagatoishi, S.Goda, T.Maruno, S.Uchiyama, K.Tsumoto. Mechanism of Dimerization and Structural Features of Human Li-Cadherin. J.Biol.Chem. 01054 2021.
ISSN: ESSN 1083-351X
PubMed: 34364873
DOI: 10.1016/J.JBC.2021.101054