Fluorine in PDB 6i77: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-4
Protein crystallography data
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
|
Fluorine Binding Sites:
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 6i77
Go back to
Fluorine Binding Sites List in 6i77
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 6i77
Go back to
Fluorine Binding Sites List in 6i77
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 6i77
Go back to
Fluorine Binding Sites List in 6i77
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 6i77
Go back to
Fluorine Binding Sites List in 6i77
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
|
|
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: Tue Jul 15 12:29:17 2025
|
