Calcium in PDB 6xiy: Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose

The structure of Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose, PDB code: 6xiy was solved by G.Birrane, P.V.Murphy, A.Gabba, J.G.Luz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.79 / 2.31
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.289, 52.289, 113.274, 90, 90, 120
R / Rfree (%)	16.2 / 20.2

The structure of Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Calcium atom in the Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose (pdb code 6xiy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose, PDB code: 6xiy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose


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 Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:30.5 occ:1.00 O A:HOH545 2.3 32.5 1.0 OE2 A:GLU224 2.3 31.7 1.0 ND2 A:ASN220 2.3 28.8 1.0 O A:HOH524 2.3 35.0 1.0 OE2 A:GLU305 2.4 36.6 1.0 O A:VAL218 2.4 29.5 1.0 OE1 A:GLU224 2.4 36.5 1.0 OE1 A:GLU305 2.4 32.3 1.0 CD A:GLU224 2.7 37.1 1.0 CD A:GLU305 2.7 39.7 1.0 C A:VAL218 3.6 30.3 1.0 CG A:ASN220 3.7 42.3 1.0 CG A:GLU224 4.2 36.0 1.0 CG A:GLU305 4.3 39.9 1.0 OH A:TYR193 4.3 32.5 1.0 CB A:VAL218 4.3 34.3 1.0 CA A:VAL218 4.4 28.4 1.0 N A:ASN220 4.4 30.9 1.0 N A:VAL218 4.4 30.6 1.0 CB A:ASN220 4.5 36.2 1.0 OD1 A:ASN220 4.5 39.5 1.0 N A:ILE219 4.5 25.4 1.0 O A:HOH517 4.5 31.5 1.0 CA A:ILE219 4.7 30.3 1.0 CG1 A:VAL218 4.7 27.4 1.0 OG A:SER191 4.8 34.9 1.0 C A:ILE219 5.0 28.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose


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 Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:28.0 occ:1.00 OD1 A:ASP293 2.3 25.1 1.0 OE1 A:GLU280 2.3 36.6 1.0 O09 A:Q3M401 2.3 34.2 1.0 OD1 A:ASN292 2.3 28.0 1.0 OD1 A:ASP269 2.4 37.8 1.0 O11 A:Q3M401 2.4 34.6 1.0 O A:ASP293 2.4 27.1 1.0 OE1 A:GLN267 2.4 28.9 1.0 CD A:GLN267 3.2 29.8 1.0 CG A:ASP269 3.3 39.8 1.0 CG A:ASP293 3.3 27.5 1.0 CG A:ASN292 3.4 32.4 1.0 CD A:GLU280 3.4 41.5 1.0 C08 A:Q3M401 3.4 34.2 1.0 C10 A:Q3M401 3.4 36.3 1.0 C A:ASP293 3.5 26.7 1.0 NE2 A:GLN267 3.5 29.8 1.0 OD2 A:ASP269 3.6 39.5 1.0 N A:ASP293 3.7 29.2 1.0 ND2 A:ASN292 3.8 28.7 1.0 OE2 A:GLU280 3.8 32.4 1.0 CA A:ASP293 4.0 27.0 1.0 OD2 A:ASP293 4.1 33.1 1.0 C12 A:Q3M401 4.2 41.3 1.0 CB A:ASP293 4.2 25.7 1.0 N A:ASP269 4.4 38.0 1.0 CG A:GLN267 4.4 28.5 1.0 CB A:ASP269 4.6 34.4 1.0 CG A:GLU280 4.6 31.1 1.0 N A:ASP294 4.6 32.1 1.0 CB A:ASN292 4.7 27.4 1.0 C A:ASN292 4.7 26.8 1.0 CB A:GLU280 4.7 28.4 1.0 C05 A:Q3M401 4.8 35.3 1.0 CB A:TRP271 4.8 31.1 1.0 CB A:GLN267 4.9 30.3 1.0 CA A:ASN292 4.9 25.9 1.0 N A:ASP270 4.9 42.7 1.0 N A:TRP271 5.0 32.2 1.0 CA A:ASP269 5.0 40.0 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose


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 Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Methyl 2-(Acetylamino)-2- Deoxy-1-Thio-Alpha-D-Galactopyranose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:51.3 occ:1.00 O A:GLU280 2.3 35.1 1.0 O A:HOH520 2.3 33.4 1.0 OD1 A:ASP281 2.4 46.5 1.0 OD1 A:ASP270 2.4 41.0 1.0 OD1 A:ASP243 2.4 41.7 1.0 OD2 A:ASP243 2.4 45.1 1.0 CG A:ASP243 2.8 40.4 1.0 CG A:ASP270 3.3 39.9 1.0 C A:GLU280 3.4 27.8 1.0 CG A:ASP281 3.6 38.4 1.0 CA A:ASP281 3.8 31.2 1.0 CB A:ASP270 3.9 37.5 1.0 N A:ASP281 4.0 29.0 1.0 O A:HOH532 4.0 36.5 1.0 OD2 A:ASP270 4.2 42.0 1.0 O A:ASP243 4.2 40.3 1.0 CB A:ASP281 4.2 33.8 1.0 CB A:ASP243 4.3 40.9 1.0 N A:GLU280 4.3 29.4 1.0 CA A:ASP270 4.5 41.9 1.0 CA A:GLU280 4.5 30.0 1.0 CZ2 A:TRP248 4.6 36.8 1.0 OD2 A:ASP281 4.6 44.0 1.0 OD2 A:ASP293 4.6 33.1 1.0 O A:HOH575 4.8 31.4 1.0 C A:ASP243 4.8 35.7 1.0 C A:ASP281 4.9 25.2 1.0

A.Gabba, A.Bogucka, J.G.Luz, A.Diniz, H.Coelho, F.Corzana, F.J.Canada, F.Marcelo, P.V.Murphy, G.Birrane. Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to Galnac and the Tumor-Associated Tn Antigen. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33724805
DOI: 10.1021/ACS.BIOCHEM.1C00009