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Fluorine in PDB 6i74: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1

Protein crystallography data

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1, PDB code: 6i74 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) 27.57 / 0.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.654, 57.781, 62.755, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 14.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1 (pdb code 6i74). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1, PDB code: 6i74:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6i74

Go back to Fluorine Binding Sites List in 6i74
Fluorine binding site 1 out of 5 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:16.2
occ:1.00
F22 A:H5Z901 0.0 16.2 1.0
C21 A:H5Z901 1.3 13.1 1.0
C23 A:H5Z901 2.3 14.1 1.0
C20 A:H5Z901 2.4 10.2 1.0
F24 A:H5Z901 2.6 17.8 1.0
N31 A:H5Z901 2.8 10.3 1.0
C19 A:H5Z901 2.9 9.6 1.0
O A:HOH1076 3.3 23.2 1.0
O A:HOH1095 3.3 28.6 1.0
HH22 A:ARG144 3.3 16.2 0.4
NH2 A:ARG144 3.5 13.5 0.4
HH21 A:ARG144 3.6 16.2 0.4
C25 A:H5Z901 3.6 13.1 1.0
C29 A:H5Z901 3.6 9.2 1.0
HH12 A:ARG144 3.6 24.4 0.6
NH1 A:ARG144 3.9 20.3 0.6
N32 A:H5Z901 4.0 9.2 1.0
C27 A:H5Z901 4.1 10.4 1.0
O A:HOH1052 4.1 12.4 1.0
CZ A:ARG144 4.1 11.8 0.4
C18 A:H5Z901 4.2 8.8 1.0
HH11 A:ARG144 4.2 24.4 0.6
HH22 A:ARG144 4.3 25.1 0.6
CZ A:ARG144 4.4 19.4 0.6
HH12 A:ARG144 4.5 12.8 0.4
O A:HOH1102 4.5 28.9 1.0
NH2 A:ARG144 4.6 20.9 0.6
NH1 A:ARG144 4.6 10.6 0.4
F26 A:H5Z901 4.6 17.1 1.0
F30 A:H5Z901 4.7 9.9 1.0
N17 A:H5Z901 4.7 8.7 1.0
NE A:ARG144 4.9 12.0 0.4
HE A:ARG144 4.9 14.4 0.4
O A:HOH1128 5.0 31.7 1.0
H181 A:H5Z901 5.0 10.5 1.0

Fluorine binding site 2 out of 5 in 6i74

Go back to Fluorine Binding Sites List in 6i74
Fluorine binding site 2 out of 5 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:17.8
occ:1.00
F24 A:H5Z901 0.0 17.8 1.0
C23 A:H5Z901 1.3 14.1 1.0
C21 A:H5Z901 2.3 13.1 1.0
C25 A:H5Z901 2.4 13.1 1.0
F22 A:H5Z901 2.6 16.2 1.0
F26 A:H5Z901 2.7 17.1 1.0
O A:HOH1095 3.2 28.6 1.0
HH22 A:ARG144 3.3 25.1 0.6
NH2 A:ARG144 3.3 20.9 0.6
O A:HOH1204 3.3 34.9 1.0
HH21 A:ARG144 3.5 25.1 0.6
HH21 A:ARG144 3.5 16.2 0.4
CZ A:ARG144 3.6 19.4 0.6
C27 A:H5Z901 3.6 10.4 1.0
HB3 A:SER237 3.6 10.4 0.3
C20 A:H5Z901 3.7 10.2 1.0
HB2 A:SER237 3.8 10.7 0.7
HH12 A:ARG144 3.9 24.4 0.6
NH1 A:ARG144 3.9 20.3 0.6
O A:HOH1128 3.9 31.7 1.0
NH2 A:ARG144 4.0 13.5 0.4
C29 A:H5Z901 4.1 9.2 1.0
OG A:SER237 4.2 7.9 0.7
NE A:ARG144 4.2 16.4 0.6
HB2 A:SER237 4.2 10.4 0.3
HE A:ARG144 4.3 14.4 0.4
HH22 A:ARG144 4.3 16.2 0.4
HE A:ARG144 4.3 19.7 0.6
CB A:SER237 4.3 8.7 0.3
CB A:SER237 4.5 8.9 0.7
HH11 A:ARG144 4.5 24.4 0.6
CZ A:ARG144 4.6 11.8 0.4
O A:HOH1113 4.6 16.9 1.0
F28 A:H5Z901 4.7 11.2 1.0
NE A:ARG144 4.7 12.0 0.4
HD2 A:ARG144 4.8 15.5 0.6
OG A:SER237 4.9 9.4 0.3
HA2 A:GLY238 4.9 8.8 1.0
C19 A:H5Z901 4.9 9.6 1.0
HB3 A:SER237 4.9 10.7 0.7
H A:GLY238 4.9 9.1 1.0
HG A:SER237 5.0 9.5 0.7

Fluorine binding site 3 out of 5 in 6i74

Go back to Fluorine Binding Sites List in 6i74
Fluorine binding site 3 out of 5 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:17.1
occ:1.00
F26 A:H5Z901 0.0 17.1 1.0
C25 A:H5Z901 1.3 13.1 1.0
C27 A:H5Z901 2.3 10.4 1.0
C23 A:H5Z901 2.3 14.1 1.0
HA2 A:GLY238 2.6 8.8 1.0
F28 A:H5Z901 2.7 11.2 1.0
F24 A:H5Z901 2.7 17.8 1.0
HB3 A:SER237 3.0 10.4 0.3
CA A:GLY238 3.0 7.3 1.0
HA3 A:GLY238 3.1 8.8 1.0
N A:GLY238 3.1 7.5 1.0
HB2 A:SER237 3.2 10.4 0.3
HB2 A:SER237 3.2 10.7 0.7
H A:GLY238 3.2 9.1 1.0
HE A:ARG144 3.3 19.7 0.6
HG3 A:ARG144 3.3 13.1 0.6
OG A:SER237 3.4 7.9 0.7
NE A:ARG144 3.4 16.4 0.6
CB A:SER237 3.5 8.7 0.3
C21 A:H5Z901 3.5 13.1 1.0
C29 A:H5Z901 3.5 9.2 1.0
HG3 A:ARG144 3.6 11.8 0.4
C A:SER237 3.6 6.9 1.0
HE A:ARG144 3.7 14.4 0.4
CB A:SER237 3.7 8.9 0.7
O A:HOH1030 3.8 30.9 1.0
CZ A:ARG144 3.8 19.4 0.6
HD2 A:ARG144 3.8 15.5 0.6
HH21 A:ARG144 3.9 25.1 0.6
NH2 A:ARG144 4.0 20.9 0.6
CD A:ARG144 4.0 12.9 0.6
O A:SER237 4.1 7.2 1.0
O A:HOH1113 4.1 16.9 1.0
CG A:ARG144 4.1 10.9 0.6
C20 A:H5Z901 4.1 10.2 1.0
HG A:SER237 4.1 9.5 0.7
NE A:ARG144 4.1 12.0 0.4
CA A:SER237 4.2 7.2 0.3
HB3 A:ALA146 4.3 8.4 1.0
CA A:SER237 4.3 7.2 0.7
O A:HOH1095 4.3 28.6 1.0
CG A:ARG144 4.4 9.8 0.4
HH21 A:ARG144 4.5 16.2 0.4
C A:GLY238 4.5 7.1 1.0
NH1 A:ARG144 4.5 20.3 0.6
HH22 A:ARG144 4.5 25.1 0.6
HA A:ILE145 4.6 7.6 1.0
H A:ALA146 4.6 7.0 1.0
HB3 A:SER237 4.6 10.7 0.7
F22 A:H5Z901 4.6 16.2 1.0
F30 A:H5Z901 4.6 9.9 1.0
HB2 A:ALA146 4.6 8.4 1.0
HG2 A:ARG144 4.6 13.1 0.6
HD2 A:ARG144 4.7 13.1 0.4
CD A:ARG144 4.7 10.9 0.4
O A:HOH1204 4.7 34.9 1.0
OG A:SER237 4.7 9.4 0.3
HH11 A:ARG144 4.7 24.4 0.6
HA A:SER237 4.7 8.7 0.3
CZ A:ARG144 4.8 11.8 0.4
HA A:SER237 4.8 8.6 0.7
O A:ARG144 4.8 8.5 1.0
HG2 A:ARG144 4.8 11.8 0.4
N A:ALA146 4.9 5.8 1.0
NH2 A:ARG144 4.9 13.5 0.4
HB2 A:ARG144 4.9 10.7 0.6
CB A:ALA146 4.9 7.0 1.0
HD3 A:ARG144 4.9 15.5 0.6
HH12 A:ARG144 5.0 24.4 0.6

Fluorine binding site 4 out of 5 in 6i74

Go back to Fluorine Binding Sites List in 6i74
Fluorine binding site 4 out of 5 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:11.2
occ:1.00
F28 A:H5Z901 0.0 11.2 1.0
C27 A:H5Z901 1.3 10.4 1.0
C25 A:H5Z901 2.3 13.1 1.0
C29 A:H5Z901 2.3 9.2 1.0
HG3 A:ARG144 2.6 11.8 0.4
F26 A:H5Z901 2.7 17.1 1.0
F30 A:H5Z901 2.7 9.9 1.0
HB2 A:ALA146 2.7 8.4 1.0
HG3 A:ARG144 2.8 13.1 0.6
HB2 A:ARG144 3.0 10.7 0.6
HD2 A:ARG144 3.1 13.1 0.4
HD2 A:ARG144 3.1 15.5 0.6
C A:ILE145 3.1 6.1 1.0
HB3 A:ALA146 3.3 8.4 1.0
N A:ALA146 3.3 5.8 1.0
CG A:ARG144 3.3 9.8 0.4
HB2 A:ARG144 3.4 10.0 0.4
CB A:ALA146 3.4 7.0 1.0
CG A:ARG144 3.4 10.9 0.6
O A:ILE145 3.4 6.2 1.0
HA A:ILE145 3.4 7.6 1.0
H A:ALA146 3.5 7.0 1.0
CD A:ARG144 3.5 10.9 0.4
N A:ILE145 3.5 6.5 1.0
HA3 A:GLY238 3.6 8.8 1.0
C23 A:H5Z901 3.6 14.1 1.0
CA A:ILE145 3.6 6.3 1.0
CB A:ARG144 3.6 8.9 0.6
CD A:ARG144 3.6 12.9 0.6
C20 A:H5Z901 3.6 10.2 1.0
HD22 A:ASN160 3.7 9.3 1.0
HD21 A:ASN160 3.7 9.3 1.0
C A:ARG144 3.8 7.3 1.0
NE A:ARG144 3.8 12.0 0.4
H A:ILE145 3.8 7.8 1.0
HE A:ARG144 3.8 14.4 0.4
CB A:ARG144 3.8 8.3 0.4
CA A:ALA146 3.9 6.2 1.0
ND2 A:ASN160 3.9 7.7 1.0
C21 A:H5Z901 4.0 13.1 1.0
HB2 A:SER237 4.1 10.4 0.3
HA2 A:GLY238 4.1 8.8 1.0
O A:ARG144 4.1 8.5 1.0
NE A:ARG144 4.1 16.4 0.6
HG2 A:ARG144 4.2 11.8 0.4
CA A:GLY238 4.2 7.3 1.0
HB1 A:ALA146 4.2 8.4 1.0
O A:SER237 4.2 7.2 1.0
OG A:SER237 4.2 7.9 0.7
HE A:ARG144 4.3 19.7 0.6
HG2 A:ARG144 4.3 13.1 0.6
HA A:ALA146 4.3 7.4 1.0
CA A:ARG144 4.3 7.2 0.6
HB3 A:ARG144 4.4 10.7 0.6
CA A:ARG144 4.5 7.3 0.4
HD3 A:ARG144 4.5 13.1 0.4
HD3 A:ARG144 4.5 15.5 0.6
C A:SER237 4.5 6.9 1.0
CZ A:ARG144 4.6 11.8 0.4
N A:GLY238 4.6 7.5 1.0
HG A:SER237 4.6 9.5 0.7
HB3 A:ARG144 4.7 10.0 0.4
F24 A:H5Z901 4.7 17.8 1.0
CZ A:ARG144 4.8 19.4 0.6
HH11 A:ARG144 4.8 24.4 0.6
HA A:ARG144 4.8 8.7 0.6
C19 A:H5Z901 4.8 9.6 1.0
HB3 A:SER237 4.9 10.4 0.3
CB A:SER237 4.9 8.7 0.3
HH11 A:ARG144 4.9 12.8 0.4
O A:HOH1023 4.9 15.5 1.0
CG A:ASN160 5.0 7.0 1.0

Fluorine binding site 5 out of 5 in 6i74

Go back to Fluorine Binding Sites List in 6i74
Fluorine binding site 5 out of 5 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:9.9
occ:1.00
F30 A:H5Z901 0.0 9.9 1.0
C29 A:H5Z901 1.3 9.2 1.0
C27 A:H5Z901 2.3 10.4 1.0
C20 A:H5Z901 2.3 10.2 1.0
H181 A:H5Z901 2.6 10.5 1.0
HB2 A:ALA146 2.6 8.4 1.0
F28 A:H5Z901 2.7 11.2 1.0
C19 A:H5Z901 2.8 9.6 1.0
C18 A:H5Z901 2.9 8.8 1.0
HD21 A:ASN160 2.9 9.3 1.0
HD2 A:ARG144 2.9 13.1 0.4
ND2 A:ASN160 3.0 7.7 1.0
HE1 A:HIS158 3.1 7.6 1.0
HD22 A:ASN160 3.3 9.3 1.0
O A:HOH1023 3.3 15.5 1.0
CG A:ASN160 3.5 7.0 1.0
CB A:ALA146 3.5 7.0 1.0
C21 A:H5Z901 3.6 13.1 1.0
C25 A:H5Z901 3.6 13.1 1.0
HD2 A:ARG144 3.6 15.5 0.6
HE2 A:HIS158 3.6 8.3 1.0
HH11 A:ARG144 3.7 12.8 0.4
OD1 A:ASN160 3.7 9.0 1.0
CE1 A:HIS158 3.8 6.3 1.0
CD A:ARG144 3.8 10.9 0.4
HB3 A:ALA146 3.8 8.4 1.0
HB1 A:ALA146 3.9 8.4 1.0
HB2 A:ARG144 3.9 10.7 0.6
NH1 A:ARG144 3.9 10.6 0.4
HB2 A:ASN160 4.0 7.4 1.0
NE2 A:HIS158 4.0 6.9 1.0
O A:HOH1052 4.0 12.4 1.0
NE A:ARG144 4.1 12.0 0.4
C23 A:H5Z901 4.1 14.1 1.0
HB2 A:ARG144 4.1 10.0 0.4
N31 A:H5Z901 4.1 10.3 1.0
CZ A:ARG144 4.1 11.8 0.4
N17 A:H5Z901 4.1 8.7 1.0
O A:ILE145 4.3 6.2 1.0
HG3 A:ARG144 4.3 11.8 0.4
HH12 A:ARG144 4.3 12.8 0.4
O15 A:H5Z901 4.3 7.0 1.0
CB A:ASN160 4.3 6.2 1.0
HD3 A:ARG144 4.5 13.1 0.4
CG A:ARG144 4.5 9.8 0.4
HE A:ARG144 4.6 14.4 0.4
CD A:ARG144 4.6 12.9 0.6
HH11 A:ARG144 4.6 24.4 0.6
CA A:ALA146 4.6 6.2 1.0
F26 A:H5Z901 4.6 17.1 1.0
C A:ILE145 4.7 6.1 1.0
F22 A:H5Z901 4.7 16.2 1.0
HA A:ALA146 4.7 7.4 1.0
N32 A:H5Z901 4.7 9.2 1.0
H151 A:H5Z901 4.7 8.4 1.0
HG3 A:ARG144 4.8 13.1 0.6
CB A:ARG144 4.8 8.9 0.6
N A:ALA146 4.8 5.8 1.0
CB A:ARG144 4.8 8.3 0.4
HA A:ASN160 4.9 6.9 1.0
NH2 A:ARG144 5.0 13.5 0.4
CG A:ARG144 5.0 10.9 0.6
ND1 A:HIS158 5.0 6.0 1.0

Reference:

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
Page generated: Thu Aug 1 21:22:08 2024

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