Calcium in PDB 4n32: Structure of Langerin Crd with Alpha-Me-Glcnac.

The structure of Structure of Langerin Crd with Alpha-Me-Glcnac., PDB code: 4n32 was solved by H.Feinberg, T.J.W.Rowntree, S.L.W.Tan, K.Drickamer, W.I.Weis, M.E.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.73 / 1.75
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	79.890, 79.890, 90.470, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23.3

The binding sites of Calcium atom in the Structure of Langerin Crd with Alpha-Me-Glcnac. (pdb code 4n32). 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 Langerin Crd with Alpha-Me-Glcnac., PDB code: 4n32:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Langerin Crd with Alpha-Me-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 Langerin Crd with Alpha-Me-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:23.8 occ:1.00 OE1 A:GLU293 2.3 21.4 1.0 OD1 A:ASP308 2.4 20.4 1.0 OE1 A:GLU285 2.4 24.0 1.0 OD1 A:ASN307 2.4 20.3 1.0 O A:ASP308 2.5 19.7 1.0 O4 A:2F8401 2.5 31.0 1.0 OD1 A:ASN287 2.5 20.7 1.0 O3 A:2F8401 2.5 30.5 1.0 CD A:GLU285 3.3 23.3 1.0 CG A:ASP308 3.3 22.5 1.0 C4 A:2F8401 3.3 22.6 1.0 CD A:GLU293 3.3 16.9 1.0 C3 A:2F8401 3.4 22.6 1.0 CG A:ASN307 3.4 16.9 1.0 CG A:ASN287 3.5 63.1 1.0 C A:ASP308 3.5 13.6 1.0 OE2 A:GLU285 3.5 24.4 1.0 OE2 A:GLU293 3.7 27.3 1.0 N A:ASP308 3.8 14.9 1.0 ND2 A:ASN307 3.8 19.1 1.0 OD2 A:ASP308 3.9 25.4 1.0 ND2 A:ASN287 4.0 35.2 1.0 CA A:ASP308 4.0 16.0 1.0 CB A:ASP308 4.2 20.7 1.0 N A:ASN287 4.3 34.8 1.0 N A:ALA289 4.5 55.2 1.0 N A:ASN288 4.5 19.4 1.0 CG A:GLU285 4.5 22.6 1.0 CB A:ALA289 4.6 35.9 1.0 CB A:ASN287 4.6 38.6 1.0 CG A:GLU293 4.6 24.4 1.0 N A:ALA309 4.7 14.1 1.0 C A:ASN307 4.7 19.1 1.0 C5 A:2F8401 4.7 30.3 1.0 C2 A:2F8401 4.7 23.1 1.0 CB A:ASN307 4.7 16.8 1.0 CB A:GLU293 4.8 23.4 1.0 CA A:ASN287 4.8 73.3 1.0 CA A:ASN307 4.9 18.0 1.0 CB A:GLU285 5.0 26.9 1.0

Calcium binding site 2 out of 4 in the Structure of Langerin Crd with Alpha-Me-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 Langerin Crd with Alpha-Me-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:20.8 occ:1.00 OD1 B:ASN287 2.4 23.1 1.0 OD1 B:ASN307 2.4 18.4 1.0 OD1 B:ASP308 2.4 17.6 1.0 OE1 B:GLU293 2.4 18.6 1.0 O3 B:2F8401 2.5 20.0 1.0 OE1 B:GLU285 2.5 22.8 1.0 O B:ASP308 2.5 19.7 1.0 O4 B:2F8401 2.5 24.9 1.0 C4 B:2F8401 3.3 22.4 1.0 CG B:ASP308 3.3 26.0 1.0 C3 B:2F8401 3.3 19.0 1.0 CD B:GLU285 3.4 23.5 1.0 CG B:ASN287 3.4 29.7 1.0 CD B:GLU293 3.4 15.1 1.0 CG B:ASN307 3.4 16.4 1.0 C B:ASP308 3.6 13.7 1.0 OE2 B:GLU285 3.7 23.7 1.0 OE2 B:GLU293 3.7 24.7 1.0 N B:ASP308 3.8 19.8 1.0 ND2 B:ASN307 3.8 16.4 1.0 OD2 B:ASP308 4.0 18.9 1.0 ND2 B:ASN287 4.0 22.4 1.0 CA B:ASP308 4.0 15.4 1.0 N B:ASN287 4.1 21.4 1.0 CB B:ASP308 4.3 16.8 1.0 CB B:ASN287 4.5 27.0 1.0 CG B:GLU285 4.6 17.9 1.0 N B:ASN288 4.6 24.7 1.0 C B:ASN307 4.7 24.3 1.0 CG B:GLU293 4.7 19.3 1.0 C2 B:2F8401 4.7 20.6 1.0 CA B:ASN287 4.7 27.1 1.0 C5 B:2F8401 4.7 34.0 1.0 CB B:ASN307 4.7 18.2 1.0 N B:ALA309 4.7 13.5 1.0 N B:ALA289 4.9 26.0 1.0 CB B:GLU293 4.9 23.4 1.0 CA B:ASN307 4.9 27.6 1.0 C B:ASN287 5.0 25.7 1.0 CB B:ALA289 5.0 20.7 1.0 CB B:GLU285 5.0 13.6 1.0

Calcium binding site 3 out of 4 in the Structure of Langerin Crd with Alpha-Me-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 Langerin Crd with Alpha-Me-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:24.4 occ:1.00 OD1 C:ASP308 2.4 22.3 1.0 OD1 C:ASN307 2.4 18.6 1.0 OD1 C:ASN287 2.4 37.5 1.0 OE1 C:GLU293 2.4 20.4 1.0 OE1 C:GLU285 2.5 24.9 1.0 O C:ASP308 2.5 24.1 1.0 O3 C:2F8401 2.5 24.6 1.0 O4 C:2F8401 2.5 23.3 1.0 C4 C:2F8401 3.2 24.1 1.0 CG C:ASN287 3.3 31.5 1.0 C3 C:2F8401 3.3 31.9 1.0 CG C:ASP308 3.3 28.2 1.0 CD C:GLU285 3.4 36.5 1.0 CD C:GLU293 3.4 19.4 1.0 CG C:ASN307 3.4 14.6 1.0 C C:ASP308 3.5 17.8 1.0 OE2 C:GLU293 3.7 21.6 1.0 OE2 C:GLU285 3.7 27.6 1.0 ND2 C:ASN307 3.8 21.2 1.0 ND2 C:ASN287 3.8 26.3 1.0 N C:ASP308 3.8 26.6 1.0 OD2 C:ASP308 4.0 26.9 1.0 CA C:ASP308 4.0 19.1 1.0 N C:ASN287 4.1 23.0 1.0 CB C:ASP308 4.3 15.9 1.0 CB C:ASN287 4.4 27.2 1.0 CG C:GLU285 4.6 26.2 1.0 N C:ASN288 4.6 25.3 1.0 C2 C:2F8401 4.6 36.5 1.0 CG C:GLU293 4.7 20.0 1.0 C5 C:2F8401 4.7 33.0 1.0 N C:ALA309 4.7 12.8 1.0 CA C:ASN287 4.7 34.4 1.0 C C:ASN307 4.7 23.4 1.0 CB C:ASN307 4.7 21.2 1.0 N C:ALA289 4.8 26.3 1.0 CB C:GLU293 4.8 21.8 1.0 O C:HOH541 4.9 30.2 1.0 CB C:ALA289 4.9 39.4 1.0 CA C:ASN307 5.0 24.4 1.0 C C:ASN287 5.0 39.6 1.0

Calcium binding site 4 out of 4 in the Structure of Langerin Crd with Alpha-Me-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 Langerin Crd with Alpha-Me-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:27.9 occ:1.00 OD1 D:ASP308 2.4 22.6 1.0 OE1 D:GLU293 2.4 23.8 1.0 OE1 D:GLU285 2.4 29.4 1.0 OD1 D:ASN307 2.5 25.7 1.0 OD1 D:ASN287 2.5 29.8 1.0 O3 D:2F8401 2.5 32.0 1.0 O4 D:2F8401 2.5 34.2 1.0 O D:ASP308 2.6 26.0 1.0 CD D:GLU285 3.3 35.5 1.0 C4 D:2F8401 3.3 39.6 1.0 C3 D:2F8401 3.3 35.6 1.0 CG D:ASP308 3.4 34.1 1.0 CD D:GLU293 3.4 22.2 1.0 CG D:ASN307 3.4 17.6 1.0 CG D:ASN287 3.4 36.6 1.0 OE2 D:GLU285 3.5 29.8 1.0 C D:ASP308 3.6 15.6 1.0 OE2 D:GLU293 3.7 34.0 1.0 ND2 D:ASN307 3.8 20.9 1.0 N D:ASP308 3.8 19.5 1.0 CA D:ASP308 4.0 15.8 1.0 ND2 D:ASN287 4.0 35.2 1.0 OD2 D:ASP308 4.1 21.8 1.0 N D:ASN287 4.1 24.1 1.0 CB D:ASP308 4.3 20.1 1.0 CB D:ASN287 4.5 36.5 1.0 CG D:GLU285 4.5 27.4 1.0 C2 D:2F8401 4.6 34.5 1.0 N D:ASN288 4.7 28.1 1.0 C5 D:2F8401 4.7 67.0 1.0 CG D:GLU293 4.7 29.4 1.0 CA D:ASN287 4.7 26.4 1.0 C D:ASN307 4.7 21.8 1.0 CB D:ASN307 4.8 27.6 1.0 N D:ALA309 4.8 13.9 1.0 N D:ALA289 4.9 32.0 1.0 CB D:ALA289 4.9 39.0 1.0 CB D:GLU293 4.9 24.7 1.0 CB D:GLU285 4.9 29.4 1.0 C D:ASN287 5.0 51.6 1.0 CA D:ASN307 5.0 20.4 1.0

H.Feinberg, T.J.Rowntree, S.L.Tan, K.Drickamer, W.I.Weis, M.E.Taylor. Common Polymorphisms in Human Langerin Change Specificity For Glycan Ligands. J.Biol.Chem. V. 288 36762 2013.
ISSN: ISSN 0021-9258
PubMed: 24217250
DOI: 10.1074/JBC.M113.528000