Calcium in PDB 7ev1: Crystal Structure of Li-Cadherin EC1-2

The structure of Crystal Structure of Li-Cadherin EC1-2, PDB code: 7ev1 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)	32.40 / 1.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.9, 79.68, 62.49, 90, 99.02, 90
R / Rfree (%)	14.3 / 18.1

The structure of Crystal Structure of Li-Cadherin EC1-2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Li-Cadherin EC1-2 (pdb code 7ev1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Li-Cadherin EC1-2, PDB code: 7ev1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:9.3 occ:1.00 OD1 A:ASN120 2.3 11.4 1.0 O A:ASN122 2.4 11.3 1.0 OD2 A:ASP215 2.4 9.8 1.0 OD2 A:ASP154 2.4 9.1 1.0 OD1 A:ASP152 2.4 10.2 1.0 O A:ASN160 2.4 9.9 1.0 OD2 A:ASP152 2.6 10.4 1.0 CG A:ASP152 2.9 9.9 1.0 CG A:ASP215 3.4 9.7 1.0 CG A:ASP154 3.4 9.2 1.0 CG A:ASN120 3.4 9.6 1.0 C A:ASN122 3.5 10.7 1.0 C A:ASN160 3.6 9.2 1.0 CB A:ASP215 3.8 8.6 1.0 CB A:ASP154 3.8 9.2 1.0 ND2 A:ASN120 4.0 9.8 1.0 N A:ASN122 4.2 10.4 1.0 CA A:ASN122 4.3 11.5 1.0 CB A:ASP152 4.4 9.8 1.0 CA A:ASN160 4.4 9.5 1.0 OD1 A:ASP215 4.5 10.4 1.0 N A:GLY161 4.5 10.8 1.0 CB A:ASN122 4.5 10.4 1.0 N A:ARG123 4.5 12.5 1.0 OD1 A:ASP154 4.6 9.1 1.0 CA A:GLY161 4.6 10.9 1.0 CB A:ASN120 4.6 9.0 1.0 CA A:ASN120 4.7 9.8 1.0 CD2 A:PHE224 4.7 14.8 1.0 CD A:PRO124 4.7 10.9 1.0 CB A:ASN160 4.7 10.0 1.0 CA A:ARG123 4.7 12.2 1.0 C A:ARG123 4.8 10.7 1.0 N A:PRO124 4.9 10.0 1.0 N A:ASP154 4.9 8.6 1.0 C A:ASN120 5.0 9.9 1.0 CA A:ASP154 5.0 9.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:9.8 occ:1.00 OD1 A:ASP154 2.3 9.1 1.0 OE2 A:GLU40 2.3 10.2 1.0 OD1 A:ASP118 2.3 10.3 1.0 OD1 A:ASP121 2.4 11.9 1.0 O A:ILE119 2.5 9.2 1.0 OE2 A:GLU87 2.5 10.0 1.0 OE1 A:GLU87 2.7 11.0 1.0 CD A:GLU87 2.9 10.8 1.0 CG A:ASP154 3.4 9.2 1.0 CG A:ASP118 3.4 10.9 1.0 CD A:GLU40 3.4 10.1 1.0 CG A:ASP121 3.5 11.6 1.0 C A:ILE119 3.7 10.4 1.0 OE1 A:GLU40 3.8 10.0 1.0 N A:ILE119 3.9 9.8 1.0 ND2 A:ASN122 3.9 10.2 1.0 OD2 A:ASP118 4.0 11.1 1.0 CA A:CA303 4.0 11.7 1.0 CB A:ASP154 4.0 9.2 1.0 OD2 A:ASP121 4.0 12.7 1.0 N A:ASP121 4.1 9.5 1.0 CA A:ASP154 4.2 9.3 1.0 OD2 A:ASP154 4.3 9.1 1.0 CG A:GLU87 4.3 11.8 1.0 CA A:ILE119 4.4 10.4 1.0 NE A:ARG86 4.5 12.0 1.0 CB A:ASP118 4.5 10.9 1.0 CA A:ASP118 4.6 11.4 1.0 CG1 A:ILE119 4.6 11.6 1.0 CB A:ASP121 4.7 11.6 1.0 CG A:GLU40 4.7 9.2 1.0 N A:ASN120 4.7 9.7 1.0 C A:ASP118 4.7 9.8 1.0 CA A:ASP121 4.8 11.4 1.0 CB A:ARG86 4.9 10.6 1.0 CA A:ASN120 4.9 9.8 1.0 O A:HOH617 5.0 13.2 1.0 N A:ASP154 5.0 8.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:11.7 occ:1.00 OE1 A:GLU87 2.3 11.0 1.0 OD1 A:ASP85 2.3 13.4 1.0 O A:HOH614 2.3 18.9 1.0 OD2 A:ASP121 2.3 12.7 1.0 OE1 A:GLU40 2.4 10.0 1.0 O A:HOH617 2.4 13.2 1.0 CG A:ASP121 3.1 11.6 1.0 OD1 A:ASP121 3.2 11.9 1.0 CD A:GLU40 3.3 10.1 1.0 CG A:ASP85 3.4 13.0 1.0 CD A:GLU87 3.6 10.8 1.0 OE2 A:GLU40 3.6 10.2 1.0 CA A:CA302 4.0 9.8 1.0 O A:HOH424 4.1 19.6 1.0 OD2 A:ASP85 4.1 13.8 1.0 CA A:ASP85 4.2 11.5 1.0 CB A:ASP85 4.2 12.0 1.0 N A:ARG86 4.3 10.2 1.0 CB A:GLU87 4.3 11.9 1.0 N A:GLU87 4.3 11.2 1.0 ND2 A:ASN122 4.4 10.2 1.0 CG A:GLU87 4.4 11.8 1.0 O A:HOH485 4.4 20.6 1.0 OE2 A:GLU87 4.4 10.0 1.0 CB A:ASP121 4.5 11.6 1.0 O A:HOH465 4.5 18.6 1.0 C A:ASP85 4.5 10.9 1.0 CG A:GLU40 4.6 9.2 1.0 O A:HOH459 4.8 21.8 1.0 CA A:GLU87 5.0 11.1 1.0 CB A:GLU40 5.0 9.3 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:9.1 occ:1.00 O B:ASN122 2.3 10.5 1.0 O B:ASN160 2.4 9.6 1.0 OD2 B:ASP215 2.4 9.4 1.0 OD2 B:ASP154 2.4 9.2 1.0 OD1 B:ASN120 2.4 11.7 1.0 OD1 B:ASP152 2.4 10.1 1.0 OD2 B:ASP152 2.6 10.9 1.0 CG B:ASP152 2.8 11.3 1.0 CG B:ASP215 3.4 9.3 1.0 CG B:ASP154 3.5 10.1 1.0 CG B:ASN120 3.5 10.8 1.0 C B:ASN122 3.5 10.5 1.0 C B:ASN160 3.6 9.1 1.0 CB B:ASP215 3.8 9.3 1.0 CB B:ASP154 3.8 9.1 1.0 ND2 B:ASN120 4.1 10.6 1.0 N B:ASN122 4.2 10.8 1.0 CA B:ASN122 4.2 11.3 1.0 CB B:ASP152 4.3 10.7 1.0 CA B:ASN160 4.4 9.6 1.0 CB B:ASN122 4.5 11.3 1.0 OD1 B:ASP215 4.5 9.5 1.0 N B:GLY161 4.5 9.6 1.0 N B:ARG123 4.6 11.9 1.0 OD1 B:ASP154 4.6 9.7 1.0 CD B:PRO124 4.6 10.4 1.0 CB B:ASN160 4.7 10.2 1.0 CA B:GLY161 4.7 11.0 1.0 CB B:ASN120 4.7 10.2 1.0 CD2 B:PHE224 4.7 14.9 1.0 CA B:ASN120 4.8 9.9 1.0 CA B:ARG123 4.8 12.0 0.6 N B:PRO124 4.8 9.8 1.0 CA B:ARG123 4.8 11.0 0.4 C B:ARG123 4.8 11.1 1.0 N B:ASP154 4.8 9.8 1.0 CA B:ASP154 5.0 9.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:9.7 occ:1.00 OD1 B:ASP154 2.3 9.7 1.0 OE2 B:GLU40 2.3 9.9 1.0 OD1 B:ASP118 2.3 9.6 1.0 OE2 B:GLU87 2.4 11.2 1.0 OD1 B:ASP121 2.4 10.9 1.0 O B:ILE119 2.5 10.2 1.0 OE1 B:GLU87 2.7 10.5 1.0 CD B:GLU87 2.8 10.1 1.0 CG B:ASP154 3.4 10.1 1.0 CD B:GLU40 3.4 10.1 1.0 CG B:ASP118 3.4 10.8 1.0 CG B:ASP121 3.5 11.7 1.0 C B:ILE119 3.7 9.8 1.0 OE1 B:GLU40 3.8 11.3 1.0 N B:ILE119 3.8 10.1 1.0 ND2 B:ASN122 4.0 11.4 1.0 CA B:CA303 4.0 13.2 1.0 CB B:ASP154 4.0 9.1 1.0 OD2 B:ASP118 4.0 11.1 1.0 OD2 B:ASP121 4.1 13.2 1.0 N B:ASP121 4.2 10.8 1.0 CA B:ASP154 4.2 9.2 1.0 CG B:GLU87 4.3 11.7 1.0 OD2 B:ASP154 4.3 9.2 1.0 CA B:ILE119 4.4 9.7 1.0 NE B:ARG86 4.4 12.2 1.0 CA B:ASP118 4.5 10.7 1.0 CB B:ASP118 4.6 10.7 1.0 CG1 B:ILE119 4.6 12.2 1.0 C B:ASP118 4.6 11.2 1.0 CB B:ASP121 4.7 10.8 1.0 CG B:GLU40 4.7 10.1 1.0 N B:ASN120 4.7 9.5 1.0 CB B:ARG86 4.9 10.8 1.0 CA B:ASP121 4.9 11.7 1.0 CA B:ASN120 4.9 9.9 1.0 NH2 B:ARG86 4.9 11.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Li-Cadherin EC1-2


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 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:13.2 occ:1.00 OE1 B:GLU87 2.3 10.5 1.0 OD1 B:ASP85 2.3 11.5 1.0 OE1 B:GLU40 2.3 11.3 1.0 OD2 B:ASP121 2.3 13.2 1.0 O B:HOH607 2.4 13.7 1.0 O B:HOH583 2.4 20.3 1.0 CG B:ASP121 3.1 11.7 1.0 OD1 B:ASP121 3.2 10.9 1.0 CD B:GLU40 3.2 10.1 1.0 CG B:ASP85 3.4 11.6 1.0 CD B:GLU87 3.5 10.1 1.0 OE2 B:GLU40 3.6 9.9 1.0 CA B:CA302 4.0 9.7 1.0 CA B:ASP85 4.2 10.6 1.0 OD2 B:ASP85 4.2 14.2 1.0 CB B:ASP85 4.2 11.6 1.0 O B:HOH503 4.2 18.7 1.0 N B:ARG86 4.2 10.5 1.0 ND2 B:ASN122 4.3 11.4 1.0 CB B:GLU87 4.3 11.0 1.0 N B:GLU87 4.3 10.6 1.0 CG B:GLU87 4.4 11.7 1.0 OE2 B:GLU87 4.4 11.2 1.0 O B:HOH455 4.4 23.6 1.0 CG B:GLU40 4.5 10.1 1.0 CB B:ASP121 4.5 10.8 1.0 C B:ASP85 4.5 10.0 1.0 O B:HOH460 4.6 21.8 1.0 O B:HOH472 4.9 23.3 1.0 CB B:GLU40 4.9 10.9 1.0 CA B:GLU87 5.0 11.2 1.0

A.Yui, J.M.M.Caaveiro, D.Kuroda, M.Nakakido, S.Nagatoishi, S.Goda, T.Maruno, S.Uchiyama, K.Tsumoto. Dimerization Mechanism and Structural Features of Human Li-Cadherin To Be Published.