Calcium in PDB 3p7f: Structure of the Human Langerin Carbohydrate Recognition Domain

The structure of Structure of the Human Langerin Carbohydrate Recognition Domain, PDB code: 3p7f was solved by A.Skerra, A.Schiefner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.20 / 2.50
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.760, 79.760, 90.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 24.3

The binding sites of Calcium atom in the Structure of the Human Langerin Carbohydrate Recognition Domain (pdb code 3p7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Human Langerin Carbohydrate Recognition Domain, PDB code: 3p7f:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Human Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:26.9 occ:1.00 OD1 A:ASN307 2.4 27.3 1.0 O A:HOH2 2.4 22.0 1.0 OE1 A:GLU285 2.5 32.1 1.0 OD1 A:ASN287 2.5 37.2 1.0 OD1 A:ASP308 2.5 29.0 1.0 OE1 A:GLU293 2.5 31.4 1.0 O A:ASP308 2.6 25.8 1.0 O A:HOH11 2.6 23.6 1.0 CG A:ASN287 3.4 38.2 1.0 CG A:ASN307 3.4 26.3 1.0 CD A:GLU285 3.4 33.0 1.0 CG A:ASP308 3.5 28.0 1.0 CD A:GLU293 3.5 32.5 1.0 C A:ASP308 3.6 25.0 1.0 N A:ASP308 3.8 24.6 1.0 OE2 A:GLU293 3.9 33.5 1.0 OE2 A:GLU285 3.9 35.0 1.0 ND2 A:ASN307 3.9 25.8 1.0 ND2 A:ASN287 3.9 36.6 1.0 CA A:ASP308 4.1 24.1 1.0 OD2 A:ASP308 4.2 30.9 1.0 N A:ASN287 4.3 35.4 1.0 CB A:ASP308 4.4 24.6 1.0 CB A:ASN287 4.6 39.1 1.0 CG A:GLU285 4.6 32.4 1.0 N A:ASN288 4.6 36.9 1.0 CB A:ASN307 4.7 26.1 1.0 C A:ASN307 4.8 24.2 1.0 N A:ALA289 4.8 39.7 1.0 N A:ALA309 4.8 24.6 1.0 CG A:GLU293 4.8 32.1 1.0 CA A:ASN287 4.9 37.9 1.0 CB A:ALA289 4.9 41.9 1.0 CA A:ASN307 5.0 25.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Human Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:30.0 occ:1.00 OD1 B:ASP308 2.3 28.4 1.0 OE1 B:GLU293 2.4 27.4 1.0 OD1 B:ASN287 2.4 34.3 1.0 OD1 B:ASN307 2.5 26.1 1.0 O B:HOH23 2.5 23.8 1.0 O B:ASP308 2.5 25.7 1.0 O B:HOH21 2.6 28.4 1.0 OE1 B:GLU285 2.6 30.7 1.0 CD B:GLU293 3.3 28.6 1.0 CG B:ASP308 3.4 27.8 1.0 CD B:GLU285 3.4 31.4 1.0 CG B:ASN307 3.5 26.4 1.0 CG B:ASN287 3.5 34.0 1.0 OE2 B:GLU293 3.5 28.4 1.0 C B:ASP308 3.6 24.3 1.0 OE2 B:GLU285 3.6 33.2 1.0 N B:ASP308 3.8 23.8 1.0 ND2 B:ASN307 3.9 27.8 1.0 ND2 B:ASN287 4.0 28.8 1.0 CA B:ASP308 4.1 23.4 1.0 OD2 B:ASP308 4.1 33.2 1.0 CB B:ASP308 4.3 24.0 1.0 N B:ASN287 4.3 31.8 1.0 O B:HOH25 4.6 31.3 1.0 CG B:GLU293 4.7 28.5 1.0 N B:ALA309 4.7 23.3 1.0 CG B:GLU285 4.7 29.2 1.0 CB B:ASN287 4.7 36.0 1.0 N B:ASN288 4.7 33.4 1.0 C B:ASN307 4.8 23.0 1.0 CB B:ASN307 4.8 25.1 1.0 N B:ALA289 4.9 37.2 1.0 CB B:ALA289 4.9 39.8 1.0 CA B:ASN287 4.9 34.4 1.0 CB B:GLU293 5.0 28.0 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Human Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:31.8 occ:1.00 O C:ASP308 2.4 26.7 1.0 OD1 C:ASP308 2.4 26.6 1.0 OE1 C:GLU285 2.5 32.8 1.0 OE1 C:GLU293 2.5 32.8 1.0 OD1 C:ASN307 2.5 24.6 1.0 O C:HOH3 2.5 25.2 1.0 O C:HOH14 2.5 31.8 1.0 OD1 C:ASN287 2.6 37.1 1.0 CG C:ASP308 3.4 28.3 1.0 CD C:GLU285 3.4 34.4 1.0 CG C:ASN287 3.5 39.6 1.0 CD C:GLU293 3.5 33.8 1.0 C C:ASP308 3.5 24.8 1.0 CG C:ASN307 3.5 25.0 1.0 OE2 C:GLU285 3.8 35.3 1.0 N C:ASP308 3.8 23.8 1.0 OE2 C:GLU293 3.8 32.8 1.0 ND2 C:ASN287 3.8 38.5 1.0 ND2 C:ASN307 3.9 26.0 1.0 CA C:ASP308 4.0 24.2 1.0 OD2 C:ASP308 4.0 31.2 1.0 CB C:ASP308 4.3 25.5 1.0 N C:ASN287 4.3 38.4 1.0 CG C:GLU285 4.5 34.8 1.0 N C:ALA309 4.6 23.7 1.0 CB C:ASN287 4.7 42.1 1.0 N C:ASN288 4.7 39.2 1.0 C C:ASN307 4.8 23.0 1.0 CG C:GLU293 4.8 33.8 1.0 CB C:ASN307 4.8 23.9 1.0 N C:ALA289 4.8 40.5 1.0 CB C:ALA289 4.9 40.6 1.0 CA C:ASN287 4.9 41.2 1.0 CB C:GLU285 4.9 34.0 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Human Langerin Carbohydrate Recognition Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1 b:35.2 occ:1.00 OE1 D:GLU293 2.4 37.5 1.0 OD1 D:ASN307 2.4 32.8 1.0 O D:ASP308 2.5 32.2 1.0 OD1 D:ASP308 2.5 38.7 1.0 O D:HOH2 2.5 37.6 1.0 OD1 D:ASN287 2.6 40.8 1.0 OE1 D:GLU285 2.7 36.4 1.0 CD D:GLU293 3.3 38.2 1.0 CG D:ASP308 3.4 33.5 1.0 CD D:GLU285 3.4 37.9 1.0 CG D:ASN307 3.5 32.4 1.0 C D:ASP308 3.5 30.2 1.0 CG D:ASN287 3.5 43.6 1.0 OE2 D:GLU293 3.7 38.3 1.0 OE2 D:GLU285 3.7 38.9 1.0 N D:ASP308 3.8 29.4 1.0 ND2 D:ASN307 3.9 32.6 1.0 OD2 D:ASP308 3.9 36.0 1.0 CA D:ASP308 4.0 28.9 1.0 ND2 D:ASN287 4.1 45.5 1.0 CB D:ASP308 4.3 29.7 1.0 N D:ASN287 4.3 40.3 1.0 N D:ALA309 4.6 29.6 1.0 CB D:ASN287 4.6 44.9 1.0 CG D:GLU293 4.7 37.0 1.0 C D:ASN307 4.7 28.6 1.0 N D:ASN288 4.7 41.7 1.0 CG D:GLU285 4.7 38.5 1.0 CB D:ASN307 4.7 31.3 1.0 N D:ALA289 4.8 45.0 1.0 CA D:ASN307 4.9 29.9 1.0 CB D:ALA289 4.9 47.4 1.0 CA D:ASN287 4.9 43.4 1.0 CB D:GLU293 4.9 34.0 1.0

L.Chatwell, A.Holla, B.B.Kaufer, A.Skerra. The Carbohydrate Recognition Domain of Langerin Reveals High Structural Similarity with the One of Dc-Sign But An Additional, Calcium-Independent Sugar-Binding Site. Mol.Immunol. V. 45 1981 2008.
ISSN: ISSN 0161-5890
PubMed: 18061677
DOI: 10.1016/J.MOLIMM.2007.10.030