Calcium in PDB 3p5f: Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man)

The structure of Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man), PDB code: 3p5f 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)	39.35 / 1.75
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.780, 79.780, 90.470, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.6

The binding sites of Calcium atom in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man) (pdb code 3p5f). 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 MAN2 (Man ALPHA1-2 Man), PDB code: 3p5f:
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 MAN2 (Man ALPHA1-2 Man)


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 MAN2 (Man ALPHA1-2 Man) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:23.2 occ:1.00 OD1 A:ASP308 2.4 18.9 1.0 OE1 A:GLU293 2.4 21.9 1.0 OD1 A:ASN307 2.4 19.7 1.0 O A:ASP308 2.5 17.5 1.0 OE1 A:GLU285 2.5 21.8 1.0 OD1 A:ASN287 2.5 20.3 1.0 O4 A:MAN402 2.5 24.3 0.5 O3 A:MAN402 2.5 10.8 0.5 O4 A:MAN402 2.5 58.2 0.5 O3 A:MAN402 2.6 21.2 0.5 C3 A:MAN402 3.3 32.5 0.5 C4 A:MAN402 3.3 19.0 0.5 CG A:ASP308 3.4 20.1 1.0 CD A:GLU285 3.4 22.9 1.0 CD A:GLU293 3.4 12.9 1.0 CG A:ASN287 3.4 54.6 1.0 C4 A:MAN402 3.4 14.2 0.5 C3 A:MAN402 3.4 14.6 0.5 CG A:ASN307 3.5 16.7 1.0 C A:ASP308 3.5 16.6 1.0 OE2 A:GLU293 3.7 23.1 1.0 OE2 A:GLU285 3.8 25.4 1.0 N A:ASP308 3.8 12.9 1.0 ND2 A:ASN307 3.8 17.4 1.0 ND2 A:ASN287 3.9 31.8 1.0 CA A:ASP308 4.0 14.2 1.0 OD2 A:ASP308 4.0 21.7 1.0 N A:ASN287 4.2 26.4 1.0 CB A:ASP308 4.3 15.9 1.0 N A:ASN288 4.5 21.7 1.0 N A:ALA289 4.5 42.5 1.0 CB A:ASN287 4.5 28.9 1.0 CG A:GLU285 4.6 28.1 1.0 CB A:ALA289 4.6 34.6 1.0 CG A:GLU293 4.7 23.6 1.0 N A:ALA309 4.7 11.0 1.0 C A:ASN307 4.7 20.9 1.0 C2 A:MAN402 4.7 30.9 0.5 C5 A:MAN402 4.7 28.2 0.5 CB A:ASN307 4.8 17.6 1.0 C5 A:MAN402 4.8 35.5 0.5 CA A:ASN287 4.8 36.6 1.0 C2 A:MAN402 4.8 16.9 0.5 CB A:GLU285 4.9 22.8 1.0 CB A:GLU293 4.9 16.4 1.0 CA A:ASN307 4.9 14.7 1.0

Calcium binding site 2 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man)


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 MAN2 (Man ALPHA1-2 Man) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:21.4 occ:1.00 OD1 B:ASP308 2.4 16.4 1.0 OD1 B:ASN287 2.4 22.2 1.0 OD1 B:ASN307 2.5 17.9 1.0 OE1 B:GLU293 2.5 20.0 1.0 O3 B:MAN402 2.5 11.6 0.5 O B:ASP308 2.5 19.1 1.0 O4 B:MAN402 2.5 26.8 0.5 O4 B:MAN402 2.5 47.3 0.5 OE1 B:GLU285 2.5 17.8 1.0 O3 B:MAN402 2.6 16.0 0.5 C3 B:MAN402 3.3 32.6 0.5 C4 B:MAN402 3.3 15.3 0.5 CG B:ASP308 3.3 21.9 1.0 CG B:ASN287 3.4 24.8 1.0 C4 B:MAN402 3.4 7.7 0.5 C3 B:MAN402 3.4 28.2 0.5 CD B:GLU285 3.4 21.0 1.0 CD B:GLU293 3.4 15.3 1.0 CG B:ASN307 3.5 16.2 1.0 C B:ASP308 3.6 16.1 1.0 OE2 B:GLU285 3.8 21.2 1.0 OE2 B:GLU293 3.8 21.1 1.0 N B:ASP308 3.8 16.8 1.0 ND2 B:ASN307 3.9 18.4 1.0 ND2 B:ASN287 3.9 23.0 1.0 OD2 B:ASP308 4.0 17.8 1.0 CA B:ASP308 4.1 13.3 1.0 N B:ASN287 4.2 21.1 1.0 CB B:ASP308 4.3 11.2 1.0 CB B:ASN287 4.5 24.9 1.0 CG B:GLU285 4.6 20.5 1.0 N B:ASN288 4.6 19.1 1.0 C2 B:MAN402 4.7 16.6 0.5 C B:ASN307 4.7 18.8 1.0 C5 B:MAN402 4.7 50.0 0.5 N B:ALA309 4.7 12.6 1.0 CA B:ASN287 4.7 23.4 1.0 CG B:GLU293 4.7 17.8 1.0 CB B:ASN307 4.8 16.2 1.0 C5 B:MAN402 4.8 26.0 0.5 C2 B:MAN402 4.8 16.6 0.5 N B:ALA289 4.9 29.3 1.0 CB B:GLU293 4.9 19.1 1.0 CA B:ASN307 5.0 26.6 1.0 C B:ASN287 5.0 28.7 1.0 O2 B:MAN402 5.0 16.7 0.5 CB B:GLU285 5.0 16.7 1.0 CB B:ALA289 5.0 23.1 1.0

Calcium binding site 3 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man)


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 MAN2 (Man ALPHA1-2 Man) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca500 b:21.2 occ:1.00 OD1 C:ASP308 2.4 18.7 1.0 OD1 C:ASN307 2.4 15.2 1.0 OE1 C:GLU293 2.4 15.5 1.0 O C:ASP308 2.5 17.5 1.0 OD1 C:ASN287 2.5 22.7 1.0 O3 C:MAN402 2.5 9.9 0.6 OE1 C:GLU285 2.5 18.6 1.0 O4 C:MAN402 2.5 17.1 0.6 O3 C:MAN450 2.6 22.4 0.4 O4 C:MAN450 2.6 58.9 0.4 C3 C:MAN402 3.3 23.4 0.6 C4 C:MAN402 3.3 16.2 0.6 CD C:GLU293 3.4 14.6 1.0 CD C:GLU285 3.4 20.6 1.0 CG C:ASP308 3.4 19.2 1.0 CG C:ASN307 3.4 11.1 1.0 C3 C:MAN450 3.4 19.5 0.4 C4 C:MAN450 3.4 21.2 0.4 CG C:ASN287 3.4 25.7 1.0 C C:ASP308 3.5 14.5 1.0 OE2 C:GLU293 3.7 19.4 1.0 OE2 C:GLU285 3.7 22.6 1.0 ND2 C:ASN307 3.8 17.5 1.0 N C:ASP308 3.8 17.4 1.0 ND2 C:ASN287 3.9 20.9 1.0 CA C:ASP308 4.0 14.2 1.0 OD2 C:ASP308 4.1 21.7 1.0 N C:ASN287 4.2 14.5 1.0 CB C:ASP308 4.3 10.5 1.0 CG C:GLU285 4.6 14.7 1.0 CB C:ASN287 4.6 21.0 1.0 CG C:GLU293 4.6 16.2 1.0 N C:ALA309 4.7 12.4 1.0 C2 C:MAN402 4.7 12.6 0.6 C C:ASN307 4.7 21.2 1.0 N C:ASN288 4.7 20.8 1.0 CB C:ASN307 4.7 14.5 1.0 C5 C:MAN402 4.7 21.9 0.6 C2 C:MAN450 4.8 30.1 0.4 CA C:ASN287 4.8 23.7 1.0 N C:ALA289 4.8 18.8 1.0 C5 C:MAN450 4.8 42.4 0.4 CB C:GLU293 4.8 19.3 1.0 CB C:ALA289 4.9 28.3 1.0 O C:HOH67 4.9 20.5 1.0 CA C:ASN307 4.9 19.3 1.0

Calcium binding site 4 out of 4 in the Structure of the Carbohydrate-Recognition Domain of Human Langerin with MAN2 (Man ALPHA1-2 Man)


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 MAN2 (Man ALPHA1-2 Man) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca500 b:24.6 occ:1.00 OD1 D:ASP308 2.4 16.3 1.0 OD1 D:ASN307 2.4 20.4 1.0 OD1 D:ASN287 2.4 24.1 1.0 OE1 D:GLU285 2.5 21.6 1.0 OE1 D:GLU293 2.5 18.6 1.0 O D:ASP308 2.5 16.3 1.0 O4 D:MAN402 2.5 16.9 0.6 O3 D:MAN402 2.5 17.1 0.6 O3 D:MAN402 2.6 33.0 0.4 O4 D:MAN402 2.6 62.0 0.4 C4 D:MAN402 3.3 9.8 0.6 C3 D:MAN402 3.3 31.9 0.6 CD D:GLU285 3.3 30.3 1.0 CG D:ASP308 3.4 20.8 1.0 CG D:ASN307 3.4 18.9 1.0 CG D:ASN287 3.4 27.1 1.0 C3 D:MAN402 3.4 39.0 0.4 C4 D:MAN402 3.4 18.8 0.4 CD D:GLU293 3.5 15.7 1.0 C D:ASP308 3.6 13.8 1.0 OE2 D:GLU285 3.7 23.7 1.0 ND2 D:ASN307 3.7 20.1 1.0 N D:ASP308 3.8 16.8 1.0 OE2 D:GLU293 3.8 23.6 1.0 ND2 D:ASN287 4.0 31.2 1.0 CA D:ASP308 4.0 18.9 1.0 OD2 D:ASP308 4.1 22.5 1.0 N D:ASN287 4.2 22.7 1.0 CB D:ASP308 4.3 12.3 1.0 CG D:GLU285 4.6 26.9 1.0 CB D:ASN287 4.6 19.7 1.0 N D:ASN288 4.6 22.1 1.0 C5 D:MAN402 4.7 33.4 0.6 C D:ASN307 4.7 15.7 1.0 N D:ALA309 4.7 14.4 1.0 C2 D:MAN402 4.7 25.9 0.6 CG D:GLU293 4.7 19.4 1.0 CB D:ASN307 4.7 15.7 1.0 CA D:ASN287 4.8 17.8 1.0 C2 D:MAN402 4.8 23.4 0.4 N D:ALA289 4.8 25.9 1.0 C5 D:MAN402 4.8 38.7 0.4 CB D:GLU293 4.9 20.0 1.0 CB D:ALA289 4.9 24.1 1.0 CB D:GLU285 5.0 27.9 1.0 O2 D:MAN402 5.0 41.6 0.6 CA D:ASN307 5.0 17.3 1.0 C D:ASN287 5.0 36.4 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