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Fluorine in PDB 6eog: Human Galectin-3C in Complex with A Galactose Derivative

Protein crystallography data

The structure of Human Galectin-3C in Complex with A Galactose Derivative, PDB code: 6eog was solved by M.Hakansson, U.J.Nilsson, F.Zetterberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.73 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.080, 58.440, 62.990, 90.00, 90.00, 90.00
R / Rfree (%) 11.2 / 14.6

Other elements in 6eog:

The structure of Human Galectin-3C in Complex with A Galactose Derivative also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 1 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:24.1
occ:0.70
F2 A:BKK1001 0.0 24.1 0.7
F2 A:BKK1001 0.1 20.5 0.3
C13 A:BKK1001 1.3 19.6 0.7
C13 A:BKK1001 1.4 18.1 0.3
C10 A:BKK1001 2.4 19.5 0.7
C10 A:BKK1001 2.4 19.1 0.3
C12 A:BKK1001 2.4 14.8 0.7
C12 A:BKK1001 2.4 14.3 0.3
F1 A:BKK1001 2.7 19.3 0.7
F1 A:BKK1001 2.8 19.0 0.3
O A:HOH1301 3.1 64.4 1.0
O A:HOH1370 3.1 36.2 1.0
NH2 A:ARG144 3.3 23.5 1.0
O A:HOH1372 3.5 43.6 1.0
C8 A:BKK1001 3.6 15.3 0.7
C8 A:BKK1001 3.6 15.0 0.3
C11 A:BKK1001 3.6 14.0 0.7
C11 A:BKK1001 3.7 14.2 0.3
OG A:SER237 3.7 13.9 1.0
CZ A:ARG144 3.7 22.2 1.0
O A:HOH1332 3.8 36.9 1.0
O A:HOH1194 3.9 45.5 1.0
CB A:SER237 4.0 12.3 1.0
NH1 A:ARG144 4.0 24.2 1.0
C9 A:BKK1001 4.1 12.0 0.7
C9 A:BKK1001 4.2 12.1 0.3
NE A:ARG144 4.4 19.4 1.0
CL A:CL1002 4.5 26.5 1.0
F A:BKK1001 4.7 15.8 0.7
F A:BKK1001 4.8 15.9 0.3
C7 A:BKK1001 4.8 16.0 0.7
C7 A:BKK1001 4.8 15.7 0.3
O A:HOH1166 4.9 19.0 1.0
N A:GLY238 5.0 10.7 1.0

Fluorine binding site 2 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 2 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:20.5
occ:0.30
F2 A:BKK1001 0.0 20.5 0.3
F2 A:BKK1001 0.1 24.1 0.7
C13 A:BKK1001 1.3 19.6 0.7
C13 A:BKK1001 1.3 18.1 0.3
C12 A:BKK1001 2.4 14.8 0.7
C12 A:BKK1001 2.4 14.3 0.3
C10 A:BKK1001 2.4 19.5 0.7
C10 A:BKK1001 2.4 19.1 0.3
F1 A:BKK1001 2.6 19.3 0.7
F1 A:BKK1001 2.7 19.0 0.3
O A:HOH1301 3.1 64.4 1.0
O A:HOH1370 3.1 36.2 1.0
NH2 A:ARG144 3.3 23.5 1.0
O A:HOH1372 3.5 43.6 1.0
C11 A:BKK1001 3.6 14.0 0.7
C8 A:BKK1001 3.6 15.3 0.7
C8 A:BKK1001 3.6 15.0 0.3
C11 A:BKK1001 3.7 14.2 0.3
OG A:SER237 3.7 13.9 1.0
CZ A:ARG144 3.7 22.2 1.0
O A:HOH1194 3.8 45.5 1.0
O A:HOH1332 3.8 36.9 1.0
CB A:SER237 3.9 12.3 1.0
NH1 A:ARG144 4.0 24.2 1.0
C9 A:BKK1001 4.1 12.0 0.7
C9 A:BKK1001 4.1 12.1 0.3
NE A:ARG144 4.4 19.4 1.0
CL A:CL1002 4.4 26.5 1.0
F A:BKK1001 4.7 15.8 0.7
F A:BKK1001 4.7 15.9 0.3
C7 A:BKK1001 4.8 16.0 0.7
C7 A:BKK1001 4.9 15.7 0.3
O A:HOH1166 4.9 19.0 1.0
N A:GLY238 4.9 10.7 1.0

Fluorine binding site 3 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 3 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:19.3
occ:0.70
F1 A:BKK1001 0.0 19.3 0.7
F1 A:BKK1001 0.0 19.0 0.3
C12 A:BKK1001 1.3 14.3 0.3
C12 A:BKK1001 1.3 14.8 0.7
C13 A:BKK1001 2.3 18.1 0.3
C13 A:BKK1001 2.4 19.6 0.7
C11 A:BKK1001 2.4 14.0 0.7
C11 A:BKK1001 2.4 14.2 0.3
F2 A:BKK1001 2.6 20.5 0.3
F A:BKK1001 2.7 15.8 0.7
F2 A:BKK1001 2.7 24.1 0.7
F A:BKK1001 2.7 15.9 0.3
CA A:GLY238 3.1 10.8 1.0
N A:GLY238 3.1 10.7 1.0
OG A:SER237 3.3 13.9 1.0
O A:HOH1194 3.3 45.5 1.0
C A:SER237 3.5 10.0 1.0
NE A:ARG144 3.5 19.4 1.0
CB A:SER237 3.6 12.3 1.0
C10 A:BKK1001 3.6 19.1 0.3
C10 A:BKK1001 3.6 19.5 0.7
C9 A:BKK1001 3.6 12.0 0.7
C9 A:BKK1001 3.6 12.1 0.3
CZ A:ARG144 3.7 22.2 1.0
NH2 A:ARG144 3.8 23.5 1.0
O A:SER237 3.9 10.0 1.0
CD A:ARG144 4.0 15.2 1.0
CG A:ARG144 4.0 14.5 1.0
C8 A:BKK1001 4.1 15.0 0.3
C8 A:BKK1001 4.1 15.3 0.7
CA A:SER237 4.2 9.6 1.0
CL A:CL1002 4.3 26.5 1.0
NH1 A:ARG144 4.4 24.2 1.0
O A:HOH1151 4.5 25.9 1.0
C A:GLY238 4.6 9.0 1.0
N A:ALA146 4.6 8.4 1.0
CB A:ALA146 4.7 9.5 1.0
O A:ARG144 4.8 11.1 1.0
O A:HOH1370 4.8 36.2 1.0
O A:HOH1301 4.8 64.4 1.0
C A:ILE145 4.9 8.0 1.0
CA A:ILE145 5.0 8.6 1.0

Fluorine binding site 4 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 4 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:19.0
occ:0.30
F1 A:BKK1001 0.0 19.0 0.3
F1 A:BKK1001 0.0 19.3 0.7
C12 A:BKK1001 1.3 14.3 0.3
C12 A:BKK1001 1.3 14.8 0.7
C13 A:BKK1001 2.4 18.1 0.3
C11 A:BKK1001 2.4 14.0 0.7
C13 A:BKK1001 2.4 19.6 0.7
C11 A:BKK1001 2.4 14.2 0.3
F2 A:BKK1001 2.7 20.5 0.3
F A:BKK1001 2.7 15.8 0.7
F A:BKK1001 2.7 15.9 0.3
F2 A:BKK1001 2.8 24.1 0.7
CA A:GLY238 3.0 10.8 1.0
N A:GLY238 3.1 10.7 1.0
OG A:SER237 3.3 13.9 1.0
O A:HOH1194 3.4 45.5 1.0
C A:SER237 3.4 10.0 1.0
NE A:ARG144 3.5 19.4 1.0
CB A:SER237 3.6 12.3 1.0
C10 A:BKK1001 3.6 19.1 0.3
C10 A:BKK1001 3.6 19.5 0.7
C9 A:BKK1001 3.6 12.0 0.7
C9 A:BKK1001 3.6 12.1 0.3
CZ A:ARG144 3.8 22.2 1.0
NH2 A:ARG144 3.8 23.5 1.0
O A:SER237 3.9 10.0 1.0
CD A:ARG144 4.0 15.2 1.0
CG A:ARG144 4.0 14.5 1.0
C8 A:BKK1001 4.1 15.0 0.3
C8 A:BKK1001 4.1 15.3 0.7
CA A:SER237 4.1 9.6 1.0
CL A:CL1002 4.3 26.5 1.0
O A:HOH1151 4.5 25.9 1.0
NH1 A:ARG144 4.5 24.2 1.0
C A:GLY238 4.5 9.0 1.0
N A:ALA146 4.6 8.4 1.0
CB A:ALA146 4.6 9.5 1.0
O A:ARG144 4.7 11.1 1.0
O A:HOH1370 4.8 36.2 1.0
O A:HOH1301 4.9 64.4 1.0
C A:ILE145 4.9 8.0 1.0
CA A:ILE145 5.0 8.6 1.0
C A:ARG144 5.0 8.9 1.0

Fluorine binding site 5 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 5 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:15.8
occ:0.70
F A:BKK1001 0.0 15.8 0.7
F A:BKK1001 0.0 15.9 0.3
C11 A:BKK1001 1.3 14.2 0.3
C11 A:BKK1001 1.4 14.0 0.7
C12 A:BKK1001 2.3 14.3 0.3
C12 A:BKK1001 2.3 14.8 0.7
C9 A:BKK1001 2.4 12.1 0.3
C9 A:BKK1001 2.4 12.0 0.7
F1 A:BKK1001 2.7 19.0 0.3
F1 A:BKK1001 2.7 19.3 0.7
C A:ILE145 3.1 8.0 1.0
CG A:ARG144 3.2 14.5 1.0
CB A:ARG144 3.3 11.9 1.0
O A:ILE145 3.4 8.2 1.0
N A:ILE145 3.4 9.1 1.0
N A:ALA146 3.4 8.4 1.0
CD A:ARG144 3.5 15.2 1.0
CB A:ALA146 3.5 9.5 1.0
CA A:ILE145 3.6 8.6 1.0
C8 A:BKK1001 3.6 15.0 0.3
C8 A:BKK1001 3.6 15.3 0.7
C A:ARG144 3.6 8.9 1.0
ND2 A:ASN160 3.6 9.9 1.0
C13 A:BKK1001 3.6 18.1 0.3
C13 A:BKK1001 3.6 19.6 0.7
NE A:ARG144 4.0 19.4 1.0
CA A:ALA146 4.0 7.2 1.0
O A:ARG144 4.1 11.1 1.0
CA A:ARG144 4.1 9.7 1.0
C10 A:BKK1001 4.1 19.1 0.3
C10 A:BKK1001 4.1 19.5 0.7
CA A:GLY238 4.4 10.8 1.0
O A:SER237 4.5 10.0 1.0
OG A:SER237 4.6 13.9 1.0
S A:SCN1006 4.6 18.8 0.8
CZ A:ARG144 4.6 22.2 1.0
F2 A:BKK1001 4.7 20.5 0.3
F2 A:BKK1001 4.7 24.1 0.7
CG A:ASN160 4.7 9.0 1.0
C A:SCN1006 4.8 25.0 0.8
C A:SER237 4.8 10.0 1.0
C7 A:BKK1001 4.8 15.7 0.3
C7 A:BKK1001 4.8 16.0 0.7
N A:GLY238 4.9 10.7 1.0
NH1 A:ARG144 4.9 24.2 1.0

Fluorine binding site 6 out of 6 in 6eog

Go back to Fluorine Binding Sites List in 6eog
Fluorine binding site 6 out of 6 in the Human Galectin-3C in Complex with A Galactose Derivative


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Galectin-3C in Complex with A Galactose Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:15.9
occ:0.30
F A:BKK1001 0.0 15.9 0.3
F A:BKK1001 0.0 15.8 0.7
C11 A:BKK1001 1.4 14.2 0.3
C11 A:BKK1001 1.4 14.0 0.7
C12 A:BKK1001 2.3 14.3 0.3
C12 A:BKK1001 2.4 14.8 0.7
C9 A:BKK1001 2.4 12.1 0.3
C9 A:BKK1001 2.4 12.0 0.7
F1 A:BKK1001 2.7 19.0 0.3
F1 A:BKK1001 2.7 19.3 0.7
C A:ILE145 3.1 8.0 1.0
CG A:ARG144 3.2 14.5 1.0
CB A:ARG144 3.3 11.9 1.0
O A:ILE145 3.3 8.2 1.0
N A:ILE145 3.4 9.1 1.0
N A:ALA146 3.4 8.4 1.0
CD A:ARG144 3.5 15.2 1.0
CB A:ALA146 3.5 9.5 1.0
CA A:ILE145 3.6 8.6 1.0
ND2 A:ASN160 3.6 9.9 1.0
C A:ARG144 3.6 8.9 1.0
C8 A:BKK1001 3.6 15.0 0.3
C8 A:BKK1001 3.6 15.3 0.7
C13 A:BKK1001 3.7 18.1 0.3
C13 A:BKK1001 3.7 19.6 0.7
CA A:ALA146 4.0 7.2 1.0
NE A:ARG144 4.0 19.4 1.0
CA A:ARG144 4.1 9.7 1.0
O A:ARG144 4.1 11.1 1.0
C10 A:BKK1001 4.1 19.1 0.3
C10 A:BKK1001 4.1 19.5 0.7
CA A:GLY238 4.5 10.8 1.0
O A:SER237 4.5 10.0 1.0
S A:SCN1006 4.6 18.8 0.8
OG A:SER237 4.6 13.9 1.0
CZ A:ARG144 4.6 22.2 1.0
F2 A:BKK1001 4.7 20.5 0.3
CG A:ASN160 4.7 9.0 1.0
F2 A:BKK1001 4.8 24.1 0.7
C A:SCN1006 4.8 25.0 0.8
C A:SER237 4.8 10.0 1.0
C7 A:BKK1001 4.8 15.7 0.3
C7 A:BKK1001 4.8 16.0 0.7
N A:GLY238 4.9 10.7 1.0
NH1 A:ARG144 4.9 24.2 1.0

Reference:

F.R.Zetterberg, K.Peterson, R.E.Johnsson, T.Brimert, M.Hakansson, D.T.Logan, H.Leffler, U.J.Nilsson. Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-Pi , and Halogen Bond Interactions. Chemmedchem V. 13 133 2018.
ISSN: ESSN 1860-7187
PubMed: 29194992
DOI: 10.1002/CMDC.201700744
Page generated: Thu Aug 1 19:45:24 2024

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