Fluorine in PDB 3gsh: Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Protein crystallography data
The structure of Three-Dimensional Structure of A Post Translational Modified Barley LTP1, PDB code: 3gsh
was solved by
M.B.Lascombe,
T.Prange,
B.Bakan,
D.Marion,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.56 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
28.740,
76.133,
39.402,
90.00,
104.34,
90.00
|
R / Rfree (%)
|
19.4 /
26.2
|
Other elements in 3gsh:
The structure of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
(pdb code 3gsh). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Three-Dimensional Structure of A Post Translational Modified Barley LTP1, PDB code: 3gsh:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 1 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:26.4
occ:1.00
|
F1
|
A:TFA301
|
0.0
|
26.4
|
1.0
|
C2
|
A:TFA301
|
1.3
|
26.0
|
1.0
|
F3
|
A:TFA301
|
2.2
|
30.4
|
1.0
|
F2
|
A:TFA301
|
2.2
|
27.2
|
1.0
|
C1
|
A:TFA301
|
2.2
|
26.7
|
1.0
|
O
|
A:TFA301
|
2.8
|
26.8
|
1.0
|
OXT
|
A:TFA301
|
3.1
|
25.3
|
1.0
|
O
|
A:LEU34
|
3.4
|
18.5
|
1.0
|
CG1
|
A:VAL47
|
3.5
|
17.2
|
1.0
|
C
|
A:LEU34
|
3.5
|
18.3
|
1.0
|
N
|
A:HIS35
|
3.6
|
18.3
|
1.0
|
CA
|
A:HIS35
|
3.7
|
19.6
|
1.0
|
CB
|
A:ALA38
|
3.7
|
34.0
|
1.0
|
O
|
A:HOH368
|
3.9
|
26.2
|
1.0
|
CB
|
A:LEU34
|
3.9
|
19.4
|
1.0
|
CB
|
A:VAL47
|
4.2
|
17.4
|
1.0
|
CA
|
A:LEU34
|
4.4
|
18.4
|
1.0
|
CG2
|
A:VAL47
|
4.4
|
19.8
|
1.0
|
CB
|
A:HIS35
|
4.6
|
19.3
|
1.0
|
OH
|
A:TYR79
|
4.7
|
19.0
|
1.0
|
C
|
A:HIS35
|
4.7
|
20.5
|
1.0
|
ND1
|
A:HIS35
|
4.9
|
16.3
|
1.0
|
CG
|
A:LEU34
|
4.9
|
21.6
|
1.0
|
O
|
A:HIS35
|
4.9
|
20.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 2 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:27.2
occ:1.00
|
F2
|
A:TFA301
|
0.0
|
27.2
|
1.0
|
C2
|
A:TFA301
|
1.3
|
26.0
|
1.0
|
F3
|
A:TFA301
|
2.1
|
30.4
|
1.0
|
F1
|
A:TFA301
|
2.2
|
26.4
|
1.0
|
C1
|
A:TFA301
|
2.3
|
26.7
|
1.0
|
O
|
A:TFA301
|
2.8
|
26.8
|
1.0
|
OH
|
A:TYR79
|
2.9
|
19.0
|
1.0
|
OXT
|
A:TFA301
|
3.1
|
25.3
|
1.0
|
O
|
A:HOH368
|
3.3
|
26.2
|
1.0
|
CG1
|
A:VAL47
|
3.5
|
17.2
|
1.0
|
CG1
|
A:VAL77
|
3.6
|
15.8
|
1.0
|
CZ
|
A:TYR79
|
3.8
|
16.3
|
1.0
|
CD1
|
A:LEU51
|
4.0
|
12.9
|
1.0
|
CG2
|
A:VAL77
|
4.1
|
18.4
|
1.0
|
CB
|
A:VAL77
|
4.4
|
17.5
|
1.0
|
CE2
|
A:TYR79
|
4.4
|
15.5
|
1.0
|
CB
|
A:VAL47
|
4.5
|
17.4
|
1.0
|
CE1
|
A:TYR79
|
4.7
|
16.2
|
1.0
|
CD
|
A:PRO78
|
4.9
|
17.9
|
1.0
|
CA
|
A:VAL77
|
4.9
|
16.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 3 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:30.4
occ:1.00
|
F3
|
A:TFA301
|
0.0
|
30.4
|
1.0
|
C2
|
A:TFA301
|
1.3
|
26.0
|
1.0
|
F2
|
A:TFA301
|
2.1
|
27.2
|
1.0
|
F1
|
A:TFA301
|
2.2
|
26.4
|
1.0
|
C1
|
A:TFA301
|
2.3
|
26.7
|
1.0
|
OXT
|
A:TFA301
|
2.5
|
25.3
|
1.0
|
CG2
|
A:VAL77
|
3.5
|
18.4
|
1.0
|
O
|
A:TFA301
|
3.5
|
26.8
|
1.0
|
N
|
A:HIS35
|
3.6
|
18.3
|
1.0
|
CA
|
A:HIS35
|
3.6
|
19.6
|
1.0
|
CB
|
A:HIS35
|
3.8
|
19.3
|
1.0
|
O
|
A:VAL31
|
3.8
|
15.0
|
1.0
|
CB
|
A:LEU34
|
4.1
|
19.4
|
1.0
|
C
|
A:LEU34
|
4.1
|
18.3
|
1.0
|
CG2
|
A:VAL31
|
4.1
|
20.4
|
1.0
|
ND1
|
A:HIS35
|
4.3
|
16.3
|
1.0
|
CG1
|
A:VAL77
|
4.3
|
15.8
|
1.0
|
CB
|
A:VAL77
|
4.4
|
17.5
|
1.0
|
CG
|
A:HIS35
|
4.5
|
18.8
|
1.0
|
O
|
A:LEU34
|
4.6
|
18.5
|
1.0
|
CG1
|
A:VAL75
|
4.7
|
15.5
|
1.0
|
CA
|
A:LEU34
|
4.8
|
18.4
|
1.0
|
CA
|
A:VAL77
|
4.8
|
16.8
|
1.0
|
CG1
|
A:VAL47
|
4.9
|
17.2
|
1.0
|
C
|
A:VAL31
|
4.9
|
16.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 4 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:33.0
occ:1.00
|
F1
|
B:TFA302
|
0.0
|
33.0
|
1.0
|
C2
|
B:TFA302
|
1.3
|
31.9
|
1.0
|
F3
|
B:TFA302
|
2.2
|
33.1
|
1.0
|
F2
|
B:TFA302
|
2.2
|
32.6
|
1.0
|
C1
|
B:TFA302
|
2.3
|
32.3
|
1.0
|
O
|
B:TFA302
|
2.5
|
31.5
|
1.0
|
CA
|
B:HIS35
|
3.1
|
21.9
|
1.0
|
CB
|
B:HIS35
|
3.2
|
22.6
|
1.0
|
N
|
B:HIS35
|
3.2
|
21.0
|
1.0
|
OXT
|
B:TFA302
|
3.4
|
32.6
|
1.0
|
O
|
B:VAL31
|
3.8
|
18.1
|
1.0
|
CG2
|
B:VAL77
|
3.8
|
19.0
|
1.0
|
C
|
B:LEU34
|
3.8
|
21.2
|
1.0
|
ND1
|
B:HIS35
|
4.1
|
21.8
|
1.0
|
CG
|
B:HIS35
|
4.1
|
22.2
|
1.0
|
CB
|
B:LEU34
|
4.3
|
20.5
|
1.0
|
O
|
B:LEU34
|
4.3
|
22.8
|
1.0
|
CG1
|
B:VAL31
|
4.5
|
21.2
|
1.0
|
C
|
B:HIS35
|
4.6
|
23.1
|
1.0
|
CA
|
B:LEU34
|
4.7
|
21.2
|
1.0
|
CB
|
B:VAL77
|
4.7
|
17.7
|
1.0
|
CG1
|
B:VAL77
|
4.8
|
18.3
|
1.0
|
CG1
|
B:VAL75
|
4.8
|
15.2
|
1.0
|
C
|
B:VAL31
|
4.9
|
19.6
|
1.0
|
O
|
B:HOH373
|
4.9
|
29.4
|
1.0
|
CA
|
B:VAL77
|
4.9
|
18.1
|
1.0
|
CG1
|
B:VAL47
|
5.0
|
17.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 5 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:32.6
occ:1.00
|
F2
|
B:TFA302
|
0.0
|
32.6
|
1.0
|
C2
|
B:TFA302
|
1.3
|
31.9
|
1.0
|
F1
|
B:TFA302
|
2.2
|
33.0
|
1.0
|
C1
|
B:TFA302
|
2.2
|
32.3
|
1.0
|
F3
|
B:TFA302
|
2.2
|
33.1
|
1.0
|
OXT
|
B:TFA302
|
2.6
|
32.6
|
1.0
|
O
|
B:TFA302
|
3.2
|
31.5
|
1.0
|
O
|
B:LEU34
|
3.4
|
22.8
|
1.0
|
O
|
B:HOH373
|
3.4
|
29.4
|
1.0
|
CA
|
B:HIS35
|
3.5
|
21.9
|
1.0
|
CG1
|
B:VAL47
|
3.6
|
17.1
|
1.0
|
C
|
B:LEU34
|
3.6
|
21.2
|
1.0
|
CB
|
B:ALA38
|
3.6
|
29.6
|
1.0
|
N
|
B:HIS35
|
3.7
|
21.0
|
1.0
|
CB
|
B:VAL47
|
4.0
|
16.9
|
1.0
|
CG2
|
B:VAL47
|
4.3
|
18.5
|
1.0
|
CB
|
B:HIS35
|
4.3
|
22.6
|
1.0
|
CB
|
B:LEU34
|
4.3
|
20.5
|
1.0
|
OH
|
B:TYR79
|
4.5
|
21.2
|
1.0
|
CA
|
B:LEU34
|
4.6
|
21.2
|
1.0
|
C
|
B:HIS35
|
4.6
|
23.1
|
1.0
|
CG
|
B:LEU34
|
4.7
|
25.6
|
1.0
|
O
|
B:HOH388
|
4.8
|
26.7
|
1.0
|
O
|
B:HIS35
|
4.8
|
22.9
|
1.0
|
ND1
|
B:HIS35
|
4.8
|
21.8
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3gsh
Go back to
Fluorine Binding Sites List in 3gsh
Fluorine binding site 6 out
of 6 in the Three-Dimensional Structure of A Post Translational Modified Barley LTP1
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Three-Dimensional Structure of A Post Translational Modified Barley LTP1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F302
b:33.1
occ:1.00
|
F3
|
B:TFA302
|
0.0
|
33.1
|
1.0
|
C2
|
B:TFA302
|
1.3
|
31.9
|
1.0
|
F1
|
B:TFA302
|
2.2
|
33.0
|
1.0
|
F2
|
B:TFA302
|
2.2
|
32.6
|
1.0
|
C1
|
B:TFA302
|
2.3
|
32.3
|
1.0
|
OXT
|
B:TFA302
|
2.9
|
32.6
|
1.0
|
OH
|
B:TYR79
|
2.9
|
21.2
|
1.0
|
O
|
B:TFA302
|
3.2
|
31.5
|
1.0
|
O
|
B:HOH373
|
3.2
|
29.4
|
1.0
|
CG1
|
B:VAL47
|
3.7
|
17.1
|
1.0
|
CG1
|
B:VAL77
|
3.8
|
18.3
|
1.0
|
CZ
|
B:TYR79
|
3.8
|
18.8
|
1.0
|
CD1
|
B:LEU51
|
4.0
|
20.0
|
1.0
|
CG2
|
B:VAL77
|
4.1
|
19.0
|
1.0
|
CE1
|
B:TYR79
|
4.4
|
18.2
|
1.0
|
CB
|
B:VAL77
|
4.4
|
17.7
|
1.0
|
CB
|
B:VAL47
|
4.6
|
16.9
|
1.0
|
CE2
|
B:TYR79
|
4.6
|
21.2
|
1.0
|
CD
|
B:PRO78
|
4.8
|
17.8
|
1.0
|
CA
|
B:VAL77
|
4.8
|
18.1
|
1.0
|
|
Reference:
B.Bakan,
M.Hamberg,
V.Larue,
T.Prange,
D.Marion,
M.B.Lascombe.
The Crystal Structure of Oxylipin-Conjugated Barley LTP1 Highlights the Unique Plasticity of the Hydrophobic Cavity of These Plant Lipid-Binding Proteins. Biochem.Biophys.Res.Commun. V. 390 780 2009.
ISSN: ISSN 0006-291X
PubMed: 19836358
DOI: 10.1016/J.BBRC.2009.10.049
Page generated: Wed Jul 31 18:58:57 2024
|