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:
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
|