Calcium in PDB 3p5i: Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac

The structure of Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac, PDB code: 3p5i was solved by H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.91 / 1.80
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.810, 79.810, 90.740, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.3

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac (pdb code 3p5i). 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 Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac, PDB code: 3p5i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac


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 Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:26.2 occ:1.00 OE1 A:GLU293 2.4 27.3 1.0 OD1 A:ASP308 2.4 25.1 1.0 OD1 A:ASN307 2.4 23.6 1.0 O A:ASP308 2.4 21.1 1.0 OE1 A:GLU285 2.5 26.9 1.0 OD1 A:ASN287 2.5 29.1 1.0 O3 A:G6S400 2.5 39.4 1.0 O4 A:G6S400 2.6 16.6 1.0 CG A:ASP308 3.3 15.8 1.0 CD A:GLU285 3.3 22.0 1.0 CD A:GLU293 3.3 24.6 1.0 CG A:ASN287 3.4 58.8 1.0 CG A:ASN307 3.5 23.5 1.0 C3 A:G6S400 3.5 32.9 1.0 C A:ASP308 3.5 22.3 1.0 C4 A:G6S400 3.5 28.6 1.0 OE2 A:GLU285 3.6 32.3 1.0 OE2 A:GLU293 3.7 29.3 1.0 N A:ASP308 3.8 16.8 1.0 ND2 A:ASN287 3.9 34.8 1.0 OD2 A:ASP308 3.9 25.2 1.0 ND2 A:ASN307 3.9 21.7 1.0 CA A:ASP308 4.0 17.3 1.0 C2 A:G6S400 4.0 40.3 1.0 CB A:ASP308 4.2 20.6 1.0 N A:ASN287 4.2 33.1 1.0 CG A:GLU285 4.6 32.6 1.0 CG A:GLU293 4.6 24.9 1.0 N A:ASN288 4.6 20.2 1.0 CB A:ASN287 4.7 46.9 1.0 N A:ALA309 4.7 17.1 1.0 N A:ALA289 4.7 44.7 1.0 CB A:GLU293 4.7 21.6 1.0 C A:ASN307 4.7 23.1 1.0 CB A:ASN307 4.8 23.4 1.0 O2 A:G6S400 4.8 43.3 1.0 C5 A:G6S400 4.8 27.2 1.0 CA A:ASN287 4.8 49.8 1.0 CB A:ALA289 4.9 32.9 1.0 CB A:GLU285 4.9 35.8 1.0 C A:ASN287 5.0 38.6 1.0

Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac


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 Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:27.4 occ:1.00 OE1 B:GLU293 2.4 29.2 1.0 OD1 B:ASP308 2.4 22.4 1.0 OD1 B:ASN307 2.4 23.0 1.0 OD1 B:ASN287 2.5 30.6 1.0 O3 B:G6S400 2.5 33.6 1.0 OE1 B:GLU285 2.5 26.8 1.0 O4 B:G6S400 2.5 26.9 1.0 O B:ASP308 2.5 27.3 1.0 CD B:GLU293 3.3 20.6 1.0 C4 B:G6S400 3.4 27.8 1.0 CG B:ASN287 3.4 42.2 1.0 CG B:ASP308 3.4 31.5 1.0 C3 B:G6S400 3.4 30.2 1.0 CD B:GLU285 3.4 27.4 1.0 CG B:ASN307 3.5 19.8 1.0 C B:ASP308 3.6 21.9 1.0 OE2 B:GLU293 3.7 31.2 1.0 OE2 B:GLU285 3.8 37.1 1.0 N B:ASP308 3.8 20.9 1.0 ND2 B:ASN287 3.9 29.3 1.0 ND2 B:ASN307 3.9 21.7 1.0 C2 B:G6S400 4.0 56.3 1.0 CA B:ASP308 4.1 13.7 1.0 OD2 B:ASP308 4.1 22.8 1.0 N B:ASN287 4.2 30.4 1.0 CB B:ASP308 4.3 15.9 1.0 CB B:ASN287 4.5 31.9 1.0 CG B:GLU285 4.6 29.0 1.0 N B:ASN288 4.6 25.7 1.0 CG B:GLU293 4.7 22.3 1.0 C B:ASN307 4.7 20.2 1.0 C5 B:G6S400 4.7 24.5 1.0 N B:ALA309 4.7 19.0 1.0 CB B:ASN307 4.7 25.2 1.0 CA B:ASN287 4.8 25.8 1.0 N B:ALA289 4.8 35.2 1.0 CB B:GLU293 4.8 21.9 1.0 O2 B:G6S400 4.9 39.1 1.0 CB B:GLU285 4.9 23.7 1.0 O B:HOH96 4.9 30.4 1.0 C B:ASN287 4.9 28.7 1.0 CB B:ALA289 5.0 32.8 1.0 CA B:ASN307 5.0 30.2 1.0

Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac


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 Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca500 b:23.8 occ:1.00 OD1 C:ASP308 2.4 22.2 1.0 OE1 C:GLU293 2.4 23.5 1.0 OE1 C:GLU285 2.4 25.1 1.0 OD1 C:ASN307 2.5 19.2 1.0 OD1 C:ASN287 2.5 33.4 1.0 O C:ASP308 2.5 19.8 1.0 O3 C:G6S400 2.5 23.6 1.0 O4 C:G6S400 2.5 26.3 1.0 CD C:GLU293 3.3 19.8 1.0 CD C:GLU285 3.3 27.1 1.0 CG C:ASP308 3.4 21.3 1.0 C3 C:G6S400 3.4 35.2 1.0 C4 C:G6S400 3.4 26.1 1.0 CG C:ASN287 3.4 25.5 1.0 CG C:ASN307 3.4 14.1 1.0 C C:ASP308 3.6 21.1 1.0 OE2 C:GLU293 3.6 25.2 1.0 OE2 C:GLU285 3.6 31.2 1.0 N C:ASP308 3.8 19.7 1.0 ND2 C:ASN307 3.9 19.1 1.0 ND2 C:ASN287 3.9 23.3 1.0 C2 C:G6S400 4.0 25.6 1.0 CA C:ASP308 4.0 21.4 1.0 OD2 C:ASP308 4.1 26.1 1.0 N C:ASN287 4.2 19.1 1.0 CB C:ASP308 4.3 13.9 1.0 CG C:GLU285 4.5 22.4 1.0 CG C:GLU293 4.6 16.2 1.0 CB C:ASN287 4.6 22.3 1.0 N C:ASN288 4.7 20.1 1.0 C C:ASN307 4.7 23.6 1.0 N C:ALA309 4.7 13.9 1.0 CB C:ASN307 4.7 16.3 1.0 O2 C:G6S400 4.7 33.5 1.0 CB C:GLU293 4.8 18.6 1.0 C5 C:G6S400 4.8 20.1 1.0 CA C:ASN287 4.8 33.8 1.0 N C:ALA289 4.9 28.2 1.0 CB C:GLU285 4.9 19.5 1.0 CA C:ASN307 5.0 20.3 1.0

Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac


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 Carbohydrate-Recognition Domain of Human Langerin with 6-SO4-Gal-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca500 b:27.4 occ:1.00 OE1 D:GLU285 2.4 22.7 1.0 OD1 D:ASP308 2.4 26.1 1.0 OE1 D:GLU293 2.4 28.5 1.0 OD1 D:ASN307 2.4 24.5 1.0 OD1 D:ASN287 2.5 34.6 1.0 O3 D:G6S400 2.5 29.3 1.0 O D:ASP308 2.5 21.9 1.0 O4 D:G6S400 2.5 31.6 1.0 CD D:GLU285 3.2 48.0 1.0 CD D:GLU293 3.4 26.8 1.0 C4 D:G6S400 3.4 41.0 1.0 CG D:ASP308 3.4 25.6 1.0 C3 D:G6S400 3.4 30.2 1.0 CG D:ASN307 3.4 21.9 1.0 CG D:ASN287 3.4 28.9 1.0 OE2 D:GLU285 3.6 26.7 1.0 C D:ASP308 3.6 18.5 1.0 OE2 D:GLU293 3.7 28.9 1.0 ND2 D:ASN307 3.8 23.4 1.0 N D:ASP308 3.8 18.8 1.0 C2 D:G6S400 4.0 42.0 1.0 ND2 D:ASN287 4.0 34.6 1.0 CA D:ASP308 4.1 18.8 1.0 OD2 D:ASP308 4.1 24.7 1.0 N D:ASN287 4.2 34.9 1.0 CB D:ASP308 4.3 19.9 1.0 CG D:GLU285 4.5 31.0 1.0 CB D:ASN287 4.6 24.3 1.0 CG D:GLU293 4.6 31.3 1.0 O2 D:G6S400 4.7 37.9 1.0 N D:ASN288 4.7 28.9 1.0 CB D:ASN307 4.7 20.3 1.0 C5 D:G6S400 4.8 29.8 1.0 N D:ALA309 4.8 16.8 1.0 CA D:ASN287 4.8 27.1 1.0 C D:ASN307 4.8 20.8 1.0 CB D:GLU293 4.8 20.4 1.0 N D:ALA289 4.8 32.3 1.0 CB D:GLU285 4.9 33.6 1.0 CB D:ALA289 4.9 29.8 1.0 O D:HOH369 5.0 39.1 1.0 C D:ASN287 5.0 49.5 1.0

H.Feinberg, M.E.Taylor, N.Razi, R.Mcbride, Y.A.Knirel, S.A.Graham, K.Drickamer, W.I.Weis. Structural Basis For Langerin Recognition of Diverse Pathogen and Mammalian Glycans Through A Single Binding Site. J.Mol.Biol. V. 405 1027 2011.
ISSN: ISSN 0022-2836
PubMed: 21112338
DOI: 10.1016/J.JMB.2010.11.039