Chlorine 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:

Calcium

(Ca)

3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 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 Chlorine with other atoms in the Cl 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:Cl405 b:47.8 occ:1.00 O A:HOH544 3.1 45.9 1.0 N A:GLN272 3.2 33.6 1.0 CA A:TRP271 3.9 32.2 1.0 CB A:GLN272 3.9 45.9 1.0 CG A:GLN272 3.9 47.2 1.0 CD1 A:TRP271 3.9 31.6 1.0 C A:TRP271 4.0 36.0 1.0 CA A:GLN272 4.1 34.5 1.0 O A:ASP270 4.5 38.3 1.0 N A:GLY273 4.5 32.4 1.0 CG A:TRP271 4.7 33.3 1.0 C A:GLN272 4.7 34.1 1.0 NE1 A:TRP271 4.8 33.6 1.0 CB A:TRP271 4.8 31.1 1.0 N A:TRP271 4.8 32.2 1.0 NE2 A:GLN272 4.9 52.1 1.0 CD A:GLN272 5.0 59.0 1.0

Chlorine binding site 2 out of 7 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 Chlorine with other atoms in the Cl 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:Cl406 b:27.5 occ:0.50 O A:HOH573 2.9 35.2 1.0 NH1 A:ARG298 3.4 27.3 1.0 CD A:ARG298 3.8 31.7 1.0 CG A:ARG298 3.8 31.0 1.0 CD A:PRO299 3.8 27.2 1.0 CB A:ARG298 4.3 33.0 1.0 CZ A:ARG298 4.4 29.0 1.0 CA A:ARG298 4.4 29.7 1.0 O A:HOH547 4.5 32.3 1.0 NE A:ARG298 4.6 27.6 1.0 CG A:PRO299 4.6 24.7 1.0 N A:PRO299 4.8 26.7 1.0 O A:HOH539 4.9 32.3 1.0

Chlorine binding site 3 out of 7 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 Chlorine with other atoms in the Cl 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:Cl407 b:34.6 occ:1.00 OG A:SER198 3.0 34.0 1.0 N A:HIS197 3.2 25.8 1.0 O A:HOH584 3.3 39.6 1.0 N A:SER198 3.6 29.6 1.0 CB A:SER198 3.7 31.4 1.0 CH2 A:TRP194 3.7 32.1 1.0 C A:HIS197 3.7 28.1 1.0 CA A:HIS197 3.8 33.5 1.0 CB A:HIS197 3.9 33.1 1.0 CZ2 A:TRP194 4.1 29.6 1.0 C A:SER196 4.1 27.6 1.0 CA A:SER196 4.1 26.4 1.0 O A:HIS197 4.2 34.2 1.0 CA A:SER198 4.3 34.0 1.0 CB A:SER196 4.3 27.9 1.0 CZ3 A:TRP194 4.8 32.1 1.0 CH2 A:TRP302 4.8 27.8 1.0 CG A:HIS197 4.9 44.9 1.0

Chlorine binding site 4 out of 7 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl408 b:40.3 occ:1.00 O A:HOH528 2.9 42.1 1.0 SG A:CYS296 3.4 34.3 0.5 N A:ASP281 3.4 29.0 1.0 N A:CYS296 3.4 27.2 1.0 SG A:CYS296 3.6 44.0 0.5 CB A:ASP281 3.6 33.8 1.0 CA A:VAL295 3.8 31.1 1.0 CG A:ASP281 3.9 38.4 1.0 OD2 A:ASP281 3.9 44.0 1.0 CB A:CYS296 4.0 33.0 0.5 CA A:ASP281 4.1 31.2 1.0 CA A:GLU280 4.1 30.0 1.0 O A:ASP294 4.1 27.3 1.0 CB A:CYS296 4.1 36.5 0.5 C A:VAL295 4.1 27.9 1.0 O A:GLY279 4.2 31.1 1.0 C A:GLU280 4.2 27.8 1.0 CA A:CYS296 4.3 28.9 0.5 CA A:CYS296 4.4 30.1 0.5 NE2 A:GLN297 4.5 34.1 0.5 CG1 A:VAL295 4.5 34.3 1.0 N A:GLU280 4.6 29.4 1.0 C A:GLY279 4.6 32.2 1.0 OD1 A:ASP281 4.6 46.5 1.0 CB A:VAL295 4.7 31.3 1.0 N A:VAL295 4.7 25.5 1.0 C A:ASP281 4.8 25.2 1.0 C A:ASP294 4.8 26.5 1.0 N A:CYS282 4.9 28.7 1.0

Chlorine binding site 5 out of 7 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl409 b:55.7 occ:1.00 N A:TRP248 3.1 41.2 1.0 CA A:ALA247 3.6 50.2 1.0 CD1 A:TRP248 3.7 34.8 1.0 C A:ALA247 3.9 39.5 1.0 O A:HOH505 3.9 42.7 1.0 CB A:ALA247 3.9 38.1 1.0 CB A:TRP248 4.0 39.7 1.0 CA A:TRP248 4.1 39.0 1.0 CE2 A:TYR256 4.2 35.0 1.0 CG A:TRP248 4.2 40.2 1.0 CD2 A:TYR256 4.3 31.0 1.0 O A:HOH558 4.6 56.2 1.0 O A:TRP248 4.6 31.3 1.0 O A:GLY246 4.8 68.1 1.0 O A:HOH574 4.8 43.1 1.0 NE1 A:TRP248 4.9 41.6 1.0 N A:ALA247 4.9 47.3 1.0 C A:TRP248 4.9 36.1 1.0

Chlorine binding site 6 out of 7 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl410 b:66.5 occ:1.00 CG A:ASP288 3.3 63.0 1.0 N A:ASP288 3.3 45.3 1.0 CB A:ASP288 3.4 57.5 1.0 OD1 A:ASP288 3.4 44.7 1.0 NZ A:LYS264 3.5 55.6 1.0 CB A:HIS286 3.7 35.8 1.0 OD2 A:ASP288 3.7 54.2 1.0 CD A:PRO287 3.9 48.2 1.0 CA A:ASP288 4.0 49.9 1.0 N A:PRO287 4.1 42.2 1.0 C A:PRO287 4.2 49.8 1.0 CB A:PRO287 4.3 51.0 1.0 ND1 A:HIS286 4.3 32.0 1.0 CA A:PRO287 4.4 49.0 1.0 CE A:LYS264 4.4 60.2 1.0 CG A:HIS286 4.5 38.1 1.0 C A:HIS286 4.5 37.1 1.0 CG A:PRO287 4.5 56.6 1.0 CA A:HIS286 4.7 31.9 1.0

Chlorine binding site 7 out of 7 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl411 b:44.5 occ:1.00 O A:HOH585 2.8 39.9 1.0 O A:HOH564 3.2 51.6 1.0 N A:TRP263 3.2 26.5 1.0 O A:HOH562 3.6 39.5 1.0 N A:ASN262 3.6 29.8 1.0 C A:GLN261 3.6 36.0 1.0 O A:GLN261 3.7 34.8 1.0 CA A:ASN262 3.8 29.4 1.0 CB A:GLN261 3.9 32.3 1.0 CD1 A:TRP263 3.9 26.2 1.0 C A:ASN262 3.9 32.9 1.0 CB A:TRP263 4.1 27.5 1.0 CA A:TRP263 4.1 28.1 1.0 O A:TRP263 4.2 34.6 1.0 CA A:GLN261 4.3 30.1 1.0 NH1 A:ARG290 4.4 34.3 1.0 CG A:TRP263 4.4 25.5 1.0 OE1 A:GLN261 4.7 47.5 1.0 C A:TRP263 4.7 29.8 1.0 O A:HOH530 4.7 28.3 1.0 O A:HOH531 4.9 37.0 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