Calcium in PDB 3c22: Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin

The structure of Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin, PDB code: 3c22 was solved by M.Thepaut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.72 / 1.50
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.555, 79.555, 90.144, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.6

The structure of Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Calcium atom in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin (pdb code 3c22). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin, PDB code: 3c22:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin


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 the Carbohydrate Recognition Domain of Human Langerin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:17.3 occ:1.00 OD1 A:ASP308 2.2 15.7 1.0 OD1 A:ASN287 2.4 18.9 1.0 OE1 A:GLU293 2.4 14.7 1.0 OD1 A:ASN307 2.4 16.3 1.0 O A:HOH481 2.5 17.9 1.0 O A:ASP308 2.5 14.8 1.0 O A:HOH482 2.6 18.0 1.0 OE1 A:GLU285 2.6 15.6 1.0 CG A:ASP308 3.1 17.4 1.0 CD A:GLU293 3.4 12.6 1.0 CG A:ASN287 3.4 19.3 1.0 CG A:ASN307 3.4 15.8 1.0 CD A:GLU285 3.5 17.6 1.0 C A:ASP308 3.6 14.2 1.0 OD2 A:ASP308 3.7 18.4 1.0 OE2 A:GLU293 3.7 17.1 1.0 ND2 A:ASN307 3.8 19.0 1.0 N A:ASP308 3.8 13.4 1.0 OE2 A:GLU285 4.0 20.1 1.0 CA A:ASP308 4.1 14.2 1.0 ND2 A:ASN287 4.1 21.7 1.0 N A:ASN287 4.1 17.6 1.0 CB A:ASP308 4.2 15.3 1.0 CB A:ASN287 4.5 18.6 1.0 N A:ASN288 4.6 20.3 1.0 CG A:GLU293 4.7 17.1 1.0 CA A:ASN287 4.7 18.8 1.0 O A:HOH405 4.7 32.5 1.0 CG A:GLU285 4.7 15.0 1.0 CB A:ASN307 4.7 12.1 1.0 N A:ALA309 4.8 13.8 1.0 N A:ALA289 4.8 20.7 1.0 C A:ASN307 4.8 12.4 1.0 CB A:ALA289 4.9 21.1 1.0 C A:ASN287 4.9 19.8 1.0 CA A:ASN307 5.0 12.4 1.0 CB A:GLU293 5.0 15.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin


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 the Carbohydrate Recognition Domain of Human Langerin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:13.7 occ:0.50 MG B:MG4 1.0 13.3 0.5 OE1 B:GLU293 2.0 22.1 1.0 OD1 B:ASP308 2.3 20.2 1.0 O B:ASP308 2.4 18.5 1.0 OD1 B:ASN287 2.4 34.7 1.0 O B:HOH458 2.5 30.0 1.0 O B:HOH457 2.7 28.7 1.0 OD1 B:ASN307 2.8 20.8 1.0 OE1 B:GLU285 3.0 21.5 1.0 CD B:GLU293 3.1 19.7 1.0 CG B:ASP308 3.1 18.9 1.0 C B:ASP308 3.4 18.1 1.0 CG B:ASN287 3.4 35.7 1.0 OE2 B:GLU293 3.4 23.0 1.0 CG B:ASN307 3.7 19.3 1.0 OD2 B:ASP308 3.8 23.7 1.0 CD B:GLU285 3.8 24.2 1.0 N B:ASP308 3.9 17.6 1.0 CA B:ASP308 4.0 17.2 1.0 ND2 B:ASN287 4.0 36.6 1.0 ND2 B:ASN307 4.0 22.8 1.0 OE2 B:GLU285 4.1 26.9 1.0 CB B:ASP308 4.1 18.9 1.0 N B:ASN287 4.2 31.4 1.0 CG B:GLU293 4.3 22.2 1.0 N B:ALA309 4.5 16.6 1.0 O B:HOH459 4.5 41.5 1.0 CB B:GLU293 4.5 22.6 1.0 CB B:ALA289 4.6 36.2 1.0 CB B:ASN287 4.6 33.4 1.0 N B:ALA289 4.7 36.1 1.0 N B:ASN288 4.7 34.4 1.0 CA B:ASN287 4.7 33.2 1.0 CA B:ALA309 4.9 16.0 1.0 C B:ASN307 4.9 17.8 1.0 C B:ASN287 4.9 34.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin


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 the Carbohydrate Recognition Domain of Human Langerin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca6 b:14.0 occ:0.50 MG C:MG7 0.9 10.4 0.5 OE1 C:GLU293 2.2 19.6 1.0 O C:HOH15 2.3 22.2 1.0 O C:ASP308 2.3 16.8 1.0 OD1 C:ASP308 2.4 17.7 1.0 OD1 C:ASN287 2.6 23.5 1.0 OD1 C:ASN307 2.7 21.0 1.0 O C:HOH16 2.8 23.0 1.0 OE1 C:GLU285 2.9 21.4 1.0 CD C:GLU293 3.0 17.8 1.0 OE2 C:GLU293 3.3 22.9 1.0 CG C:ASP308 3.3 18.8 1.0 C C:ASP308 3.4 17.2 1.0 CG C:ASN307 3.5 19.6 1.0 CG C:ASN287 3.6 25.1 1.0 ND2 C:ASN307 3.7 20.2 1.0 N C:ASP308 3.8 16.4 1.0 CD C:GLU285 3.9 22.6 1.0 CA C:ASP308 4.0 16.7 1.0 OD2 C:ASP308 4.0 20.1 1.0 CB C:ASP308 4.2 17.9 1.0 ND2 C:ASN287 4.3 29.2 1.0 OE2 C:GLU285 4.3 24.3 1.0 N C:ASN287 4.3 22.1 1.0 CG C:GLU293 4.4 20.4 1.0 N C:ALA309 4.5 16.8 1.0 CB C:GLU293 4.6 18.3 1.0 N C:ASN288 4.6 24.9 1.0 O C:HOH17 4.7 32.1 1.0 N C:ALA289 4.7 27.3 1.0 CB C:ALA289 4.7 27.9 1.0 CB C:ASN287 4.7 23.3 1.0 C C:ASN307 4.8 16.3 1.0 CA C:ASN287 4.9 23.8 1.0 CB C:ASN307 4.9 16.0 1.0 CA C:ALA309 4.9 17.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Carbohydrate Recognition Domain of Human Langerin


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 the Carbohydrate Recognition Domain of Human Langerin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca9 b:20.6 occ:1.00 OD1 D:ASP308 2.4 19.3 1.0 OD1 D:ASN287 2.4 23.8 1.0 OD1 D:ASN307 2.4 19.5 1.0 OE1 D:GLU293 2.5 20.5 1.0 O D:HOH434 2.5 22.4 1.0 OE1 D:GLU285 2.6 23.1 1.0 O D:ASP308 2.6 17.7 1.0 O D:HOH433 2.6 25.1 1.0 CG D:ASP308 3.4 18.8 1.0 CG D:ASN307 3.4 17.4 1.0 CG D:ASN287 3.4 25.1 1.0 CD D:GLU293 3.5 20.1 1.0 CD D:GLU285 3.5 24.3 1.0 C D:ASP308 3.6 16.5 1.0 ND2 D:ASN307 3.7 22.7 1.0 OE2 D:GLU293 3.8 20.5 1.0 N D:ASP308 3.9 18.2 1.0 OE2 D:GLU285 3.9 24.6 1.0 ND2 D:ASN287 4.0 24.2 1.0 OD2 D:ASP308 4.1 20.6 1.0 CA D:ASP308 4.1 16.9 1.0 N D:ASN287 4.1 22.1 1.0 CB D:ASP308 4.3 17.4 1.0 CB D:ASN287 4.6 23.6 1.0 N D:ASN288 4.6 24.4 1.0 CG D:GLU285 4.7 22.1 1.0 CA D:ASN287 4.7 23.4 1.0 CB D:ASN307 4.7 16.7 1.0 CG D:GLU293 4.7 19.6 1.0 O D:HOH547 4.8 38.9 1.0 N D:ALA309 4.8 16.8 1.0 C D:ASN307 4.8 17.4 1.0 O D:HOH435 4.8 43.2 1.0 N D:ALA289 4.9 25.4 1.0 C D:ASN287 5.0 24.2 1.0 CB D:GLU293 5.0 19.1 1.0 CA D:ASN307 5.0 17.4 1.0

M.Thepaut, J.Valladeau, A.Nurisso, R.Kahn, B.Arnou, C.Vives, S.Saeland, C.Ebel, C.Monnier, C.Dezutter-Dambuyant, A.Imberty, F.Fieschi. Structural Studies of Langerin and Birbeck Granule: A Macromolecular Organization Model Biochemistry V. 48 2684 2009.
ISSN: ISSN 0006-2960
PubMed: 19175323
DOI: 10.1021/BI802151W