Fluorine in PDB 6i75: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2, PDB code: 6i75 was solved by R.Kumar, K.Peterson, U.J.Nilsson, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.84 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.380, 57.598, 60.887, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.1

The binding sites of Fluorine atom in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2 (pdb code 6i75). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2, PDB code: 6i75:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:22.7 occ:1.00 F20 A:H5T301 0.0 22.7 1.0 C19 A:H5T301 1.3 22.0 1.0 C18 A:H5T301 2.2 21.8 1.0 C21 A:H5T301 2.3 24.9 1.0 H161 A:H5T301 2.6 22.7 1.0 C17 A:H5T301 2.7 20.3 1.0 F22 A:H5T301 2.7 26.7 1.0 HB2 A:ALA146 2.7 14.2 1.0 C16 A:H5T301 2.8 18.9 1.0 HD21 A:ASN160 3.1 11.6 1.0 HE1 A:HIS158 3.2 10.0 1.0 HD2 A:ARG144 3.3 26.1 1.0 ND2 A:ASN160 3.3 9.7 1.0 C27 A:H5T301 3.4 26.1 1.0 O A:HOH473 3.4 28.0 1.0 CB A:ALA146 3.5 11.8 1.0 C23 A:H5T301 3.6 26.7 1.0 HD22 A:ASN160 3.7 11.6 1.0 CG A:ASN160 3.7 8.6 1.0 HB1 A:ALA146 3.7 14.2 1.0 HB3 A:ALA146 3.8 14.2 1.0 OD1 A:ASN160 3.9 10.4 1.0 CE1 A:HIS158 3.9 8.3 1.0 C25 A:H5T301 4.0 28.4 1.0 O A:HOH451 4.0 34.2 1.0 N29 A:H5T301 4.0 22.0 1.0 N15 A:H5T301 4.1 17.9 1.0 HH11 A:ARG144 4.2 39.7 1.0 NE2 A:HIS158 4.2 10.2 1.0 HB2 A:ARG144 4.3 16.0 1.0 CD A:ARG144 4.3 21.7 1.0 HB2 A:ASN160 4.3 8.7 1.0 O13 A:H5T301 4.4 11.7 1.0 F28 A:H5T301 4.4 29.8 1.0 HG3 A:ARG144 4.6 20.8 1.0 NH1 A:ARG144 4.6 33.1 1.0 CB A:ASN160 4.7 7.2 1.0 N30 A:H5T301 4.7 21.6 1.0 O A:ILE145 4.7 8.2 1.0 H131 A:H5T301 4.8 14.1 1.0 O24 A:H5T301 4.8 26.9 1.0 CA A:ALA146 4.8 8.8 1.0 HD3 A:ARG144 4.9 26.1 1.0 CG A:ARG144 4.9 17.3 1.0 NE A:ARG144 4.9 27.4 1.0 HA A:ALA146 4.9 10.5 1.0 H241 A:H5T301 5.0 32.3 1.0

Fluorine binding site 2 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:26.7 occ:1.00 F22 A:H5T301 0.0 26.7 1.0 C21 A:H5T301 1.3 24.9 1.0 C19 A:H5T301 2.4 22.0 1.0 C23 A:H5T301 2.4 26.7 1.0 HG3 A:ARG144 2.5 20.8 1.0 HB2 A:ALA146 2.6 14.2 1.0 F20 A:H5T301 2.7 22.7 1.0 HD2 A:ARG144 2.8 26.1 1.0 O24 A:H5T301 2.8 26.9 1.0 H241 A:H5T301 2.9 32.3 1.0 HB3 A:ALA146 3.1 14.2 1.0 CG A:ARG144 3.2 17.3 1.0 CB A:ALA146 3.3 11.8 1.0 HB2 A:ARG144 3.3 16.0 1.0 CD A:ARG144 3.3 21.7 1.0 C25 A:H5T301 3.6 28.4 1.0 N A:ALA146 3.6 8.8 1.0 C A:ILE145 3.6 8.2 1.0 C18 A:H5T301 3.6 21.8 1.0 NE A:ARG144 3.7 27.4 1.0 HD21 A:ASN160 3.8 11.6 1.0 H A:ALA146 3.8 10.6 1.0 CB A:ARG144 3.8 13.3 1.0 HE A:ARG144 3.8 33.0 1.0 HA3 A:GLY238 3.9 11.9 1.0 HB2 A:SER237 3.9 15.5 0.5 O A:ILE145 3.9 8.2 1.0 HA2 A:GLY238 3.9 11.9 1.0 HA A:ILE145 3.9 11.0 1.0 HD22 A:ASN160 4.0 11.6 1.0 C27 A:H5T301 4.0 26.1 1.0 CA A:ALA146 4.0 8.8 1.0 HB1 A:ALA146 4.0 14.2 1.0 HG2 A:ARG144 4.1 20.8 1.0 ND2 A:ASN160 4.1 9.7 1.0 N A:ILE145 4.1 9.4 1.0 OG A:SER237 4.1 13.2 0.5 CA A:ILE145 4.1 9.2 1.0 C A:ARG144 4.2 10.7 1.0 HD3 A:ARG144 4.2 26.1 1.0 HG A:SER237 4.3 15.8 0.5 CA A:GLY238 4.3 9.9 1.0 CZ A:ARG144 4.3 32.5 1.0 O A:SER237 4.4 9.7 1.0 H A:ILE145 4.4 11.3 1.0 HA A:ALA146 4.5 10.5 1.0 HB3 A:ARG144 4.5 16.0 1.0 O A:HOH473 4.5 28.0 1.0 HH11 A:ARG144 4.5 39.7 1.0 C A:SER237 4.6 8.5 1.0 N A:GLY238 4.6 10.4 1.0 O A:ARG144 4.6 11.2 1.0 NH1 A:ARG144 4.7 33.1 1.0 F26 A:H5T301 4.7 32.2 1.0 CA A:ARG144 4.7 10.5 1.0 CB A:SER237 4.8 12.9 0.5 C17 A:H5T301 4.8 20.3 1.0 HB3 A:SER237 4.9 15.5 0.5

Fluorine binding site 3 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:32.2 occ:1.00 F26 A:H5T301 0.0 32.2 1.0 C25 A:H5T301 1.3 28.4 1.0 C23 A:H5T301 2.4 26.7 1.0 C27 A:H5T301 2.4 26.1 1.0 F28 A:H5T301 2.7 29.8 1.0 O24 A:H5T301 2.8 26.9 1.0 HH22 A:ARG144 3.3 42.5 1.0 H241 A:H5T301 3.4 32.3 1.0 NH2 A:ARG144 3.4 35.4 1.0 HH21 A:ARG144 3.6 42.5 1.0 C21 A:H5T301 3.6 24.9 1.0 C18 A:H5T301 3.7 21.8 1.0 CZ A:ARG144 3.9 32.5 1.0 C19 A:H5T301 4.0 22.0 1.0 HH12 A:ARG144 4.1 39.7 1.0 HB3 A:SER237 4.1 15.5 0.5 NH1 A:ARG144 4.2 33.1 1.0 HB2 A:SER237 4.4 15.5 0.5 OG A:SER237 4.4 13.2 0.5 HB2 A:SER237 4.5 15.5 0.5 NE A:ARG144 4.6 27.4 1.0 HE A:ARG144 4.7 33.0 1.0 F22 A:H5T301 4.7 26.7 1.0 CB A:SER237 4.7 12.9 0.5 HH11 A:ARG144 4.8 39.7 1.0 C17 A:H5T301 4.9 20.3 1.0 CB A:SER237 4.9 12.9 0.5

Fluorine binding site 4 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:29.8 occ:1.00 F28 A:H5T301 0.0 29.8 1.0 C27 A:H5T301 1.3 26.1 1.0 C18 A:H5T301 2.3 21.8 1.0 C25 A:H5T301 2.4 28.4 1.0 N29 A:H5T301 2.7 22.0 1.0 C17 A:H5T301 2.7 20.3 1.0 F26 A:H5T301 2.7 32.2 1.0 C19 A:H5T301 3.4 22.0 1.0 C23 A:H5T301 3.6 26.7 1.0 O A:HOH451 3.9 34.2 1.0 HH12 A:ARG144 3.9 39.7 1.0 N30 A:H5T301 3.9 21.6 1.0 C16 A:H5T301 4.0 18.9 1.0 C21 A:H5T301 4.0 24.9 1.0 NH1 A:ARG144 4.2 33.1 1.0 F20 A:H5T301 4.4 22.7 1.0 HH11 A:ARG144 4.5 39.7 1.0 HH22 A:ARG144 4.5 42.5 1.0 N15 A:H5T301 4.6 17.9 1.0 CZ A:ARG144 4.7 32.5 1.0 O24 A:H5T301 4.8 26.9 1.0 NH2 A:ARG144 4.8 35.4 1.0 H161 A:H5T301 4.8 22.7 1.0

R.Kumar, K.Peterson, M.Misini Ignjatovic, H.Leffler, U.Ryde, U.J.Nilsson, D.T.Logan. Substituted Polyfluoroaryl Interactions with An Arginine Side Chain in Galectin-3 Are Governed By Steric-, Desolvation and Electronic Conjugation Effects. Org. Biomol. Chem. V. 17 1081 2019.
ISSN: ESSN 1477-0539
PubMed: 30632578
DOI: 10.1039/C8OB02888E