Calcium in PDB 5duv: Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose

The structure of Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose, PDB code: 5duv was solved by K.Bum-Erdene, H.Blanchard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.24 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.920, 64.750, 64.470, 90.00, 91.26, 90.00
R / Rfree (%)	15.5 / 19.9

The binding sites of Calcium atom in the Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose (pdb code 5duv). 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 Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose, PDB code: 5duv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose


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 Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:19.6 occ:1.00 O A:HOH368 2.0 23.5 1.0 O A:GLY70 2.1 18.9 1.0 OD1 A:ASP72 2.2 17.3 1.0 O A:PHE68 2.3 20.8 1.0 O A:HOH315 2.3 27.2 1.0 O A:HOH378 2.6 34.7 1.0 C A:GLY70 3.3 20.9 1.0 CG A:ASP72 3.4 16.5 1.0 C A:PHE68 3.5 19.7 1.0 N A:ASP72 3.8 17.4 1.0 N A:GLY70 3.9 20.4 1.0 OD2 A:ASP72 4.1 16.5 1.0 CA A:GLY70 4.2 21.6 1.0 CA A:PHE68 4.2 18.8 1.0 C A:ASP69 4.2 20.9 1.0 C A:TRP71 4.3 21.6 1.0 N A:TRP71 4.3 24.1 1.0 O A:HOH309 4.3 23.0 1.0 CA A:ASP72 4.4 17.3 1.0 N A:ASP69 4.5 21.8 1.0 CA A:TRP71 4.5 28.5 1.0 CB A:ASP72 4.5 16.3 1.0 CA A:ASP69 4.6 21.8 1.0 CB A:PHE68 4.6 17.2 1.0 O A:ASP69 4.7 20.8 1.0 CD1 A:PHE68 4.9 18.8 1.0 O A:TRP71 5.0 19.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose


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 Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:25.3 occ:1.00 O B:HOH376 2.1 28.9 1.0 O B:GLY70 2.2 26.5 1.0 O B:PHE68 2.3 30.1 1.0 O B:HOH372 2.4 31.9 1.0 OD1 B:ASP72 2.4 24.9 1.0 O B:HOH384 2.5 36.8 1.0 O B:HOH374 3.4 42.4 1.0 C B:PHE68 3.4 32.1 1.0 C B:GLY70 3.4 27.3 1.0 CG B:ASP72 3.6 33.6 1.0 N B:GLY70 3.9 26.8 1.0 CA B:PHE68 4.1 25.8 1.0 OD2 B:ASP72 4.1 29.9 1.0 CA B:GLY70 4.1 25.6 1.0 N B:ASP72 4.2 29.0 1.0 CB B:PHE68 4.4 27.3 1.0 C B:ASP69 4.4 27.6 1.0 N B:ASP69 4.5 29.1 1.0 N B:TRP71 4.5 26.1 1.0 CD1 B:PHE68 4.6 29.3 1.0 CA B:ASP69 4.7 31.3 1.0 C B:TRP71 4.7 31.8 1.0 CA B:ASP72 4.8 27.0 1.0 CA B:TRP71 4.8 30.5 1.0 CB B:ASP72 4.8 27.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose


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 Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:17.3 occ:1.00 O C:HOH365 2.1 28.3 1.0 O C:GLY70 2.2 15.5 1.0 O C:HOH314 2.3 14.1 1.0 O C:PHE68 2.3 19.4 1.0 OD1 C:ASP72 2.3 20.0 1.0 O C:ACT203 2.9 28.2 1.0 CG C:ASP72 3.4 21.6 1.0 C C:GLY70 3.4 14.4 1.0 C C:PHE68 3.4 18.1 1.0 C C:ACT203 3.9 28.5 1.0 N C:GLY70 3.9 16.9 1.0 N C:ASP72 4.0 16.5 1.0 O C:HOH307 4.0 28.4 1.0 OD2 C:ASP72 4.0 23.0 1.0 CA C:PHE68 4.1 17.2 1.0 CA C:GLY70 4.2 15.4 1.0 OXT C:ACT203 4.2 31.6 1.0 O C:HOH377 4.4 38.0 1.0 N C:TRP71 4.5 14.9 1.0 C C:ASP69 4.5 19.1 1.0 CB C:PHE68 4.5 20.4 1.0 CA C:ASP72 4.5 17.2 1.0 N C:ASP69 4.5 16.8 1.0 CB C:ASP72 4.5 19.6 1.0 C C:TRP71 4.6 16.1 1.0 CA C:TRP71 4.7 16.8 1.0 CA C:ASP69 4.8 21.3 1.0 CD1 C:PHE68 4.9 24.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose


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 Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:11.9 occ:1.00 O D:GLY70 2.3 11.2 1.0 O D:PHE68 2.3 13.4 1.0 O D:HOH396 2.3 15.9 1.0 O D:HOH365 2.4 11.6 1.0 O D:HOH400 2.4 14.5 1.0 OD1 D:ASP72 2.4 13.1 1.0 O D:ACT203 3.2 27.1 1.0 C D:PHE68 3.5 12.9 1.0 CG D:ASP72 3.5 14.4 1.0 C D:GLY70 3.5 10.7 1.0 N D:GLY70 3.9 11.5 1.0 O D:HOH323 4.0 15.5 1.0 OD2 D:ASP72 4.0 16.2 1.0 N D:ASP72 4.1 12.0 1.0 C D:ACT203 4.1 24.0 1.0 CA D:PHE68 4.2 11.5 1.0 O D:HOH364 4.2 28.1 1.0 O B:HOH337 4.3 32.7 1.0 CA D:GLY70 4.3 11.0 1.0 O B:HOH318 4.3 10.4 1.0 OXT D:ACT203 4.4 21.6 1.0 C D:ASP69 4.4 13.3 1.0 N D:ASP69 4.5 12.0 1.0 N D:TRP71 4.5 10.5 1.0 CB D:PHE68 4.6 12.7 1.0 CA D:ASP72 4.6 12.2 1.0 CB D:ASP72 4.6 13.3 1.0 CA D:ASP69 4.7 14.2 1.0 CD1 D:PHE68 4.7 14.3 1.0 CA D:TRP71 4.7 11.5 1.0 C D:TRP71 4.8 12.9 1.0

K.Bum-Erdene, H.Leffler, U.J.Nilsson, H.Blanchard. Structural Characterisation of Human Galectin-4 N-Terminal Carbohydrate Recognition Domain in Complex with Glycerol, Lactose, 3'-Sulfo-Lactose, and 2'-Fucosyllactose. Sci Rep V. 6 20289 2016.
ISSN: ESSN 2045-2322
PubMed: 26828567
DOI: 10.1038/SREP20289