Fluorine in PDB 6i77: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-4

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-4, PDB code: 6i77 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)	31.42 / 1.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.888, 57.409, 62.836, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 20

The binding sites of Fluorine atom in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-4 (pdb code 6i77). 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-4, PDB code: 6i77:
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-4


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-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:24.0 occ:1.00 F20 A:H5Q301 0.0 24.0 1.0 C19 A:H5Q301 1.3 23.3 1.0 C18 A:H5Q301 2.3 23.4 1.0 C21 A:H5Q301 2.4 24.9 1.0 HB2 A:ALA146 2.7 13.7 1.0 F22 A:H5Q301 2.7 27.6 1.0 H161 A:H5Q301 2.7 22.7 1.0 C17 A:H5Q301 2.8 21.5 1.0 HD2 A:ARG144 2.9 23.2 0.5 C16 A:H5Q301 3.0 19.0 1.0 HD21 A:ASN160 3.0 12.8 1.0 HE1 A:HIS158 3.1 12.8 1.0 ND2 A:ASN160 3.2 10.7 1.0 O A:HOH506 3.4 23.6 0.7 HD22 A:ASN160 3.4 12.8 1.0 HH11 A:ARG144 3.5 27.9 0.5 HD2 A:ARG144 3.5 22.1 0.5 O A:HOH506 3.5 20.1 0.3 C27 A:H5Q301 3.5 27.4 1.0 CB A:ALA146 3.6 11.4 1.0 CG A:ASN160 3.6 10.0 1.0 C23 A:H5Q301 3.7 27.0 1.0 HE2 A:HIS158 3.8 14.0 1.0 NH1 A:ARG144 3.8 23.3 0.5 O A:HOH434 3.8 21.5 1.0 CE1 A:HIS158 3.8 10.7 1.0 CD A:ARG144 3.8 19.3 0.5 OD1 A:ASN160 3.8 11.7 1.0 HB1 A:ALA146 3.8 13.7 1.0 HB3 A:ALA146 3.9 13.7 1.0 HB2 A:ARG144 4.0 17.5 0.5 C25 A:H5Q301 4.0 28.8 1.0 HB2 A:ASN160 4.1 11.4 1.0 N29 A:H5Q301 4.1 21.9 1.0 NE2 A:HIS158 4.1 11.7 1.0 CZ A:ARG144 4.1 23.4 0.5 NE A:ARG144 4.1 21.9 0.5 HH12 A:ARG144 4.2 27.9 0.5 HB2 A:ARG144 4.2 15.8 0.5 N15 A:H5Q301 4.3 18.8 1.0 HG3 A:ARG144 4.3 19.5 0.5 CD A:ARG144 4.4 18.5 0.5 O A:ILE145 4.4 10.0 1.0 HD3 A:ARG144 4.4 23.2 0.5 CB A:ASN160 4.5 9.5 1.0 O13 A:H5Q301 4.5 12.9 1.0 CG A:ARG144 4.6 16.3 0.5 F28 A:H5Q301 4.6 28.9 1.0 HH11 A:ARG144 4.7 28.3 0.5 CA A:ALA146 4.7 10.1 1.0 HE A:ARG144 4.7 26.2 0.5 HG3 A:ARG144 4.7 19.4 0.5 N30 A:H5Q301 4.8 22.2 1.0 HA A:ALA146 4.8 12.1 1.0 CB A:ARG144 4.8 14.6 0.5 N24 A:H5Q301 4.9 27.2 1.0 C A:ILE145 4.9 11.3 1.0 CB A:ARG144 4.9 13.2 0.5 CG A:ARG144 4.9 16.2 0.5 N A:ALA146 5.0 9.8 1.0 HD3 A:ARG144 5.0 22.1 0.5 H131 A:H5Q301 5.0 15.4 1.0

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


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-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:27.6 occ:1.00 F22 A:H5Q301 0.0 27.6 1.0 C21 A:H5Q301 1.3 24.9 1.0 C23 A:H5Q301 2.4 27.0 1.0 C19 A:H5Q301 2.4 23.3 1.0 HG3 A:ARG144 2.6 19.5 0.5 HG3 A:ARG144 2.6 19.4 0.5 F20 A:H5Q301 2.7 24.0 1.0 HB2 A:ALA146 2.7 13.7 1.0 HD2 A:ARG144 2.8 22.1 0.5 N24 A:H5Q301 2.8 27.2 1.0 HD2 A:ARG144 3.0 23.2 0.5 HB2 A:ARG144 3.0 17.5 0.5 H242 A:H5Q301 3.1 32.6 1.0 CG A:ARG144 3.2 16.2 0.5 HB3 A:ALA146 3.3 13.7 1.0 CG A:ARG144 3.3 16.3 0.5 CD A:ARG144 3.3 18.5 0.5 HB2 A:ARG144 3.4 15.8 0.5 CB A:ALA146 3.4 11.4 1.0 H241 A:H5Q301 3.4 32.6 1.0 CD A:ARG144 3.5 19.3 0.5 C A:ILE145 3.5 11.3 1.0 N A:ALA146 3.5 9.8 1.0 C25 A:H5Q301 3.6 28.8 1.0 CB A:ARG144 3.6 14.6 0.5 C18 A:H5Q301 3.7 23.4 1.0 H A:ALA146 3.7 11.7 1.0 O A:ILE145 3.7 10.0 1.0 HA3 A:GLY238 3.8 14.9 1.0 NE A:ARG144 3.8 21.9 0.5 NE A:ARG144 3.8 21.3 0.5 HA A:ILE145 3.8 14.3 1.0 HD21 A:ASN160 3.9 12.8 1.0 CB A:ARG144 3.9 13.2 0.5 HA2 A:GLY238 3.9 14.9 1.0 HE A:ARG144 3.9 26.2 0.5 HE A:ARG144 3.9 25.5 0.5 HD22 A:ASN160 3.9 12.8 1.0 N A:ILE145 3.9 11.7 1.0 CA A:ILE145 4.0 11.9 1.0 C A:ARG144 4.0 13.1 1.0 HB2 A:SER237 4.0 15.1 0.5 CA A:ALA146 4.1 10.1 1.0 C27 A:H5Q301 4.1 27.4 1.0 HG2 A:ARG144 4.1 19.5 0.5 ND2 A:ASN160 4.1 10.7 1.0 HG2 A:ARG144 4.1 19.4 0.5 OG A:SER237 4.2 13.2 0.5 CA A:GLY238 4.2 12.4 1.0 HB1 A:ALA146 4.2 13.7 1.0 HD3 A:ARG144 4.2 22.1 0.5 H A:ILE145 4.2 14.1 1.0 O A:ARG144 4.3 12.8 1.0 HB3 A:ARG144 4.4 17.5 0.5 O A:SER237 4.4 11.1 1.0 HD3 A:ARG144 4.4 23.2 0.5 CA A:ARG144 4.5 13.6 0.5 CZ A:ARG144 4.5 23.4 0.5 HA A:ALA146 4.5 12.1 1.0 HG A:SER237 4.5 15.8 0.5 C A:SER237 4.5 11.6 1.0 N A:GLY238 4.5 11.6 1.0 HB3 A:SER237 4.5 15.1 0.5 CZ A:ARG144 4.6 22.7 0.5 CA A:ARG144 4.6 13.1 0.5 O A:HOH506 4.6 23.6 0.7 HB3 A:ARG144 4.7 15.8 0.5 F26 A:H5Q301 4.7 31.5 1.0 HH11 A:ARG144 4.7 27.9 0.5 CB A:SER237 4.7 12.5 0.5 HH11 A:ARG144 4.8 28.3 0.5 NH1 A:ARG144 4.9 23.3 0.5 C17 A:H5Q301 4.9 21.5 1.0 HB2 A:SER237 4.9 15.6 0.5 O A:HOH425 5.0 28.8 1.0 NH1 A:ARG144 5.0 23.6 0.5 O A:HOH434 5.0 21.5 1.0

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


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-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:31.5 occ:1.00 F26 A:H5Q301 0.0 31.5 1.0 C25 A:H5Q301 1.3 28.8 1.0 C23 A:H5Q301 2.4 27.0 1.0 C27 A:H5Q301 2.4 27.4 1.0 F28 A:H5Q301 2.7 28.9 1.0 N24 A:H5Q301 2.8 27.2 1.0 H241 A:H5Q301 3.1 32.6 1.0 NH2 A:ARG144 3.3 23.5 0.5 HH22 A:ARG144 3.4 28.1 0.5 H242 A:H5Q301 3.4 32.6 1.0 HH21 A:ARG144 3.4 28.1 0.5 C21 A:H5Q301 3.6 24.9 1.0 O A:HOH456 3.6 35.9 1.0 CZ A:ARG144 3.7 22.7 0.5 C18 A:H5Q301 3.7 23.4 1.0 HH21 A:ARG144 3.8 29.2 0.5 C19 A:H5Q301 4.1 23.3 1.0 HB3 A:SER237 4.1 15.1 0.5 NH2 A:ARG144 4.2 24.3 0.5 NH1 A:ARG144 4.2 23.6 0.5 HH12 A:ARG144 4.2 28.3 0.5 NE A:ARG144 4.2 21.3 0.5 HE A:ARG144 4.3 25.5 0.5 HB2 A:SER237 4.3 15.6 0.5 HH22 A:ARG144 4.4 29.2 0.5 HE A:ARG144 4.6 26.2 0.5 OG A:SER237 4.6 13.2 0.5 F22 A:H5Q301 4.7 27.6 1.0 HH11 A:ARG144 4.7 28.3 0.5 CZ A:ARG144 4.7 23.4 0.5 HB2 A:SER237 4.8 15.1 0.5 CB A:SER237 4.9 12.5 0.5 NE A:ARG144 4.9 21.9 0.5 HD2 A:ARG144 4.9 22.1 0.5 C17 A:H5Q301 4.9 21.5 1.0 CB A:SER237 4.9 13.0 0.5

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


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-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:28.9 occ:1.00 F28 A:H5Q301 0.0 28.9 1.0 C27 A:H5Q301 1.3 27.4 1.0 C18 A:H5Q301 2.3 23.4 1.0 C25 A:H5Q301 2.4 28.8 1.0 F26 A:H5Q301 2.7 31.5 1.0 C17 A:H5Q301 2.8 21.5 1.0 N29 A:H5Q301 2.8 21.9 1.0 C19 A:H5Q301 3.5 23.3 1.0 HH22 A:ARG144 3.7 29.2 0.5 C23 A:H5Q301 3.7 27.0 1.0 NH2 A:ARG144 3.9 24.3 0.5 N30 A:H5Q301 4.0 22.2 1.0 C21 A:H5Q301 4.1 24.9 1.0 C16 A:H5Q301 4.1 19.0 1.0 O A:HOH434 4.1 21.5 1.0 HH21 A:ARG144 4.1 29.2 0.5 HH12 A:ARG144 4.1 28.3 0.5 O A:HOH461 4.2 38.3 1.0 NH1 A:ARG144 4.3 23.6 0.5 CZ A:ARG144 4.4 23.4 0.5 HH12 A:ARG144 4.4 27.9 0.5 F20 A:H5Q301 4.6 24.0 1.0 NH1 A:ARG144 4.6 23.3 0.5 HH11 A:ARG144 4.6 28.3 0.5 HH22 A:ARG144 4.6 28.1 0.5 N15 A:H5Q301 4.7 18.8 1.0 CZ A:ARG144 4.7 22.7 0.5 NH2 A:ARG144 4.8 23.5 0.5 N24 A:H5Q301 4.8 27.2 1.0 H161 A:H5Q301 4.9 22.7 1.0 O A:HOH456 5.0 35.9 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