Bromine in PDB 7cxd: Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group

The structure of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group, PDB code: 7cxd was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.17 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.241, 58.712, 70.773, 90, 113.85, 90
R / Rfree (%)	22.6 / 24.8

The structure of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

The binding sites of Bromine atom in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group (pdb code 7cxd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group, PDB code: 7cxd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Br301 b:32.5 occ:0.60 CD1 A:ILE249 2.7 40.9 1.0 ND2 A:ASN160 3.3 22.9 1.0 NZ A:LYS162 3.6 36.0 1.0 CA A:GLY247 3.9 20.0 1.0 CG1 A:ILE249 3.9 26.5 1.0 CB A:ASN160 4.0 18.5 1.0 CE A:LYS162 4.0 40.3 1.0 CD A:LYS162 4.1 38.8 1.0 CG A:ASN160 4.1 24.6 1.0 C A:GLY247 4.4 19.6 1.0 OD1 A:ASP131 4.6 33.8 1.0 O A:GLY247 4.7 19.6 1.0 N A:GLY247 4.9 19.2 1.0

Bromine binding site 2 out of 5 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Br301 b:43.7 occ:0.80 ND2 B:ASN160 3.4 27.6 1.0 NZ B:LYS162 3.6 46.2 1.0 CA B:GLY247 3.9 21.7 1.0 CE B:LYS162 4.0 45.7 1.0 CG2 B:ILE249 4.0 29.6 1.0 CB B:ASN160 4.1 20.5 1.0 CD B:LYS162 4.1 47.6 1.0 CG B:ASN160 4.3 34.7 1.0 C B:GLY247 4.4 23.1 1.0 OD1 B:ASP131 4.6 40.2 1.0 O B:GLY247 4.8 24.9 1.0 CD1 B:ILE249 4.8 44.4 1.0 N B:GLY247 4.9 23.3 1.0

Bromine binding site 3 out of 5 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Br301 b:30.6 occ:0.90 NZ D:LYS162 3.3 60.5 1.0 ND2 D:ASN160 3.4 24.6 1.0 CA D:GLY247 3.7 15.2 1.0 CE D:LYS162 3.8 44.0 1.0 O D:HOH423 3.8 39.4 1.0 CB D:ASN160 3.9 17.2 1.0 CD D:LYS162 4.0 31.1 1.0 CG D:ASN160 4.2 25.6 1.0 CG2 D:ILE249 4.3 26.9 1.0 C D:GLY247 4.3 18.0 1.0 N D:GLY247 4.6 16.0 1.0 O D:GLY247 4.7 19.4 1.0 CG D:LYS162 4.9 34.3 1.0

Bromine binding site 4 out of 5 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Br302 b:64.3 occ:0.50 O D:PRO129 3.3 24.0 1.0 O D:HOH406 3.7 41.7 1.0 CB D:PRO129 4.2 26.1 1.0 O D:HOH426 4.2 35.4 1.0 C D:PRO129 4.2 24.9 1.0 OD2 D:ASP131 4.2 29.3 1.0 CD D:PRO129 4.4 26.1 1.0 CG D:PRO129 4.6 30.9 1.0 CA D:PRO129 4.7 23.9 1.0 N D:PRO129 4.8 24.2 1.0

Bromine binding site 5 out of 5 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ E:Br301 b:34.2 occ:0.95 NZ E:LYS162 3.6 34.8 1.0 ND2 E:ASN160 3.6 21.6 1.0 CA E:GLY247 3.7 22.4 1.0 CE E:LYS162 3.9 40.3 1.0 CB E:ASN160 4.1 18.0 1.0 CD E:LYS162 4.1 34.7 1.0 CG2 E:ILE249 4.1 28.6 1.0 C E:GLY247 4.3 22.6 1.0 CG E:ASN160 4.4 26.2 1.0 N E:GLY247 4.6 23.4 1.0 O E:GLY247 4.6 21.2 1.0 N E:ILE248 5.0 18.7 1.0

A.Kumar, M.Paul, M.Panda, S.Jayaram, N.Kalidindi, H.Sale, M.Vetrichelvan, A.Gupta, A.Mathur, B.Beno, A.Regueiro-Ren, D.Cheng, M.Ramarao, K.Ghosh. Molecular Mechanism of Interspecies Differences in the Binding Affinity of TD139 to Galectin-3. Glycobiology 2021.
ISSN: ESSN 1460-2423
PubMed: 34228782
DOI: 10.1093/GLYCOB/CWAB072