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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:

Zinc (Zn) 4 atoms
Sodium (Na) 3 atoms

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

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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: Sun Dec 13 11:47:12 2020

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