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Fluorine in PDB 6j63: Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc

Enzymatic activity of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc:
1.13.11.27;

Protein crystallography data

The structure of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc, PDB code: 6j63 was solved by W.C.Yang, G.F.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.19 / 2.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.660, 95.960, 97.930, 90.00, 92.15, 90.00
R / Rfree (%) 27.8 / 30.1

Other elements in 6j63:

The structure of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc (pdb code 6j63). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc, PDB code: 6j63:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6j63

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Fluorine binding site 1 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:19.2
occ:1.00
 F2 A:NTD502 0.0 19.2 1.0
C14 A:NTD502 1.4 19.7 1.0
F1 A:NTD502 2.2 18.3 1.0
F3 A:NTD502 2.2 19.9 1.0
C11 A:NTD502 2.4 20.0 1.0
C10 A:NTD502 3.2 21.5 1.0
C12 A:NTD502 3.2 19.8 1.0
CE1 A:PHE424 3.3 26.5 1.0
CD1 A:PHE424 3.3 26.5 1.0
CZ A:PHE424 3.4 28.5 1.0
CG A:PHE424 3.5 25.9 1.0
CE2 A:PHE424 3.6 29.3 1.0
CD2 A:PHE424 3.6 28.1 1.0
N A:PHE424 3.9 24.0 1.0
CA A:PHE424 4.0 25.0 1.0
CB A:PHE424 4.4 25.4 1.0
C A:ASN423 4.4 24.7 1.0
C9 A:NTD502 4.4 21.8 1.0
C13 A:NTD502 4.4 19.1 1.0
CB A:ASN423 4.6 25.7 1.0
O A:ASN423 4.8 20.1 1.0
O A:GLY420 4.9 21.9 1.0
C8 A:NTD502 4.9 20.6 1.0

Fluorine binding site 2 out of 12 in 6j63

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Fluorine binding site 2 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:19.9
occ:1.00
 F3 A:NTD502 0.0 19.9 1.0
C14 A:NTD502 1.4 19.7 1.0
F1 A:NTD502 2.2 18.3 1.0
F2 A:NTD502 2.2 19.2 1.0
C11 A:NTD502 2.4 20.0 1.0
C12 A:NTD502 2.8 19.8 1.0
CD1 A:LEU368 3.2 22.8 1.0
CB A:ASN423 3.5 25.7 1.0
C10 A:NTD502 3.6 21.5 1.0
C13 A:NTD502 4.1 19.1 1.0
CE1 A:PHE381 4.3 18.7 1.0
NE2 A:GLN379 4.3 15.9 1.0
CG A:ASN423 4.4 25.9 1.0
C A:ASN423 4.5 24.7 1.0
CG A:LEU368 4.6 21.8 1.0
CA A:ASN423 4.6 24.9 1.0
N A:PHE424 4.6 24.0 1.0
C9 A:NTD502 4.7 21.8 1.0
O A:GLY420 4.7 21.9 1.0
CD1 A:LEU427 4.7 37.1 1.0
O A:ASN423 4.8 20.1 1.0
ND2 A:ASN423 4.8 26.3 1.0
CD2 A:LEU368 4.9 22.2 1.0
C8 A:NTD502 4.9 20.6 1.0
CD1 A:PHE381 5.0 18.6 1.0
CE1 A:PHE424 5.0 26.5 1.0
CD1 A:PHE424 5.0 26.5 1.0

Fluorine binding site 3 out of 12 in 6j63

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Fluorine binding site 3 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:18.3
occ:1.00
 F1 A:NTD502 0.0 18.3 1.0
C14 A:NTD502 1.4 19.7 1.0
F3 A:NTD502 2.2 19.9 1.0
F2 A:NTD502 2.2 19.2 1.0
C11 A:NTD502 2.3 20.0 1.0
C10 A:NTD502 2.7 21.5 1.0
C12 A:NTD502 3.6 19.8 1.0
C9 A:NTD502 4.1 21.8 1.0
CE1 A:PHE381 4.2 18.7 1.0
CD1 A:LEU368 4.4 22.8 1.0
CD1 A:PHE381 4.4 18.6 1.0
C13 A:NTD502 4.7 19.1 1.0
C8 A:NTD502 4.9 20.6 1.0
CZ A:PHE424 4.9 28.5 1.0
N A:NTD502 4.9 22.6 1.0
CZ A:PHE381 4.9 18.6 1.0

Fluorine binding site 4 out of 12 in 6j63

Go back to Fluorine Binding Sites List in 6j63
Fluorine binding site 4 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:20.5
occ:1.00
 F2 B:NTD502 0.0 20.5 1.0
C14 B:NTD502 1.4 20.2 1.0
F1 B:NTD502 2.2 18.3 1.0
F3 B:NTD502 2.2 22.9 1.0
C11 B:NTD502 2.3 20.9 1.0
C10 B:NTD502 2.7 23.2 1.0
C12 B:NTD502 3.6 21.9 1.0
CZ B:PHE424 3.8 29.7 1.0
CE2 B:PHE424 3.8 30.3 1.0
CE1 B:PHE424 4.0 29.1 1.0
C9 B:NTD502 4.1 25.5 1.0
CD2 B:PHE424 4.1 30.0 1.0
CD1 B:PHE424 4.3 29.4 1.0
CG B:PHE424 4.4 29.1 1.0
CD1 B:LEU427 4.5 29.9 1.0
C13 B:NTD502 4.7 22.6 1.0
C8 B:NTD502 4.9 22.9 1.0
N B:NTD502 5.0 30.9 1.0

Fluorine binding site 5 out of 12 in 6j63

Go back to Fluorine Binding Sites List in 6j63
Fluorine binding site 5 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:22.9
occ:1.00
 F3 B:NTD502 0.0 22.9 1.0
C14 B:NTD502 1.4 20.2 1.0
F1 B:NTD502 2.2 18.3 1.0
F2 B:NTD502 2.2 20.5 1.0
C11 B:NTD502 2.4 20.9 1.0
C12 B:NTD502 2.7 21.9 1.0
N B:PHE424 3.3 23.8 1.0
CB B:ASN423 3.4 24.6 1.0
C B:ASN423 3.5 26.4 1.0
CD1 B:PHE424 3.6 29.4 1.0
C10 B:NTD502 3.6 23.2 1.0
CE1 B:PHE424 3.8 29.1 1.0
CD1 B:LEU427 3.8 29.9 1.0
CA B:PHE424 3.9 25.4 1.0
CG B:PHE424 3.9 29.1 1.0
CA B:ASN423 4.0 23.9 1.0
O B:ASN423 4.0 29.1 1.0
C13 B:NTD502 4.1 22.6 1.0
O B:GLY420 4.1 24.4 1.0
CZ B:PHE424 4.3 29.7 1.0
CD2 B:PHE424 4.4 30.0 1.0
CB B:PHE424 4.5 27.4 1.0
CE2 B:PHE424 4.5 30.3 1.0
N B:ASN423 4.6 21.5 1.0
CD1 B:LEU368 4.6 24.4 1.0
CG B:ASN423 4.6 25.2 1.0
C9 B:NTD502 4.7 25.5 1.0
C8 B:NTD502 4.9 22.9 1.0

Fluorine binding site 6 out of 12 in 6j63

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Fluorine binding site 6 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:18.3
occ:1.00
 F1 B:NTD502 0.0 18.3 1.0
C14 B:NTD502 1.4 20.2 1.0
F2 B:NTD502 2.2 20.5 1.0
F3 B:NTD502 2.2 22.9 1.0
C11 B:NTD502 2.3 20.9 1.0
C10 B:NTD502 3.1 23.2 1.0
CD1 B:LEU368 3.2 24.4 1.0
C12 B:NTD502 3.2 21.9 1.0
CE1 B:PHE381 3.7 20.3 1.0
CD1 B:LEU427 3.7 29.9 1.0
CD1 B:PHE381 4.2 20.2 1.0
C9 B:NTD502 4.4 25.5 1.0
C13 B:NTD502 4.4 22.6 1.0
CB B:ASN423 4.6 24.6 1.0
CG B:LEU368 4.6 23.9 1.0
CZ B:PHE381 4.7 19.1 1.0
OE1 B:GLN379 4.9 17.6 1.0
C8 B:NTD502 4.9 22.9 1.0
CD2 B:LEU368 5.0 24.3 1.0

Fluorine binding site 7 out of 12 in 6j63

Go back to Fluorine Binding Sites List in 6j63
Fluorine binding site 7 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:18.1
occ:1.00
 F2 C:NTD502 0.0 18.1 1.0
C14 C:NTD502 1.4 21.2 1.0
F3 C:NTD502 2.2 20.7 1.0
F1 C:NTD502 2.2 23.3 1.0
C11 C:NTD502 2.3 23.7 1.0
C10 C:NTD502 2.7 26.4 1.0
C12 C:NTD502 3.5 24.8 1.0
CE2 C:PHE381 3.8 24.7 1.0
CD1 C:LEU368 4.1 22.4 1.0
C9 C:NTD502 4.1 27.5 1.0
CD2 C:PHE381 4.2 23.7 1.0
CD1 C:LEU427 4.2 24.4 1.0
CZ C:PHE381 4.7 24.0 1.0
C13 C:NTD502 4.7 24.2 1.0
C8 C:NTD502 4.9 24.6 1.0
N C:NTD502 5.0 32.8 1.0

Fluorine binding site 8 out of 12 in 6j63

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Fluorine binding site 8 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:20.7
occ:1.00
 F3 C:NTD502 0.0 20.7 1.0
C14 C:NTD502 1.4 21.2 1.0
F2 C:NTD502 2.2 18.1 1.0
F1 C:NTD502 2.2 23.3 1.0
C11 C:NTD502 2.4 23.7 1.0
C10 C:NTD502 3.1 26.4 1.0
C12 C:NTD502 3.3 24.8 1.0
CE1 C:PHE424 3.3 23.9 1.0
CD1 C:PHE424 3.4 24.7 1.0
CZ C:PHE424 3.5 24.0 1.0
CG C:PHE424 3.5 23.5 1.0
CE2 C:PHE424 3.7 24.0 1.0
CD2 C:PHE424 3.7 23.4 1.0
N C:PHE424 3.9 23.6 1.0
CA C:PHE424 4.1 23.1 1.0
CD1 C:LEU427 4.3 24.4 1.0
C9 C:NTD502 4.4 27.5 1.0
CB C:PHE424 4.4 23.3 1.0
C C:ASN423 4.4 23.2 1.0
C13 C:NTD502 4.5 24.2 1.0
CB C:ASN423 4.6 23.1 1.0
O C:ASN423 4.8 23.8 1.0
O C:GLY420 4.9 23.2 1.0
C8 C:NTD502 4.9 24.6 1.0

Fluorine binding site 9 out of 12 in 6j63

Go back to Fluorine Binding Sites List in 6j63
Fluorine binding site 9 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:23.3
occ:1.00
 F1 C:NTD502 0.0 23.3 1.0
C14 C:NTD502 1.4 21.2 1.0
F3 C:NTD502 2.2 20.7 1.0
F2 C:NTD502 2.2 18.1 1.0
C11 C:NTD502 2.3 23.7 1.0
C12 C:NTD502 2.7 24.8 1.0
CD1 C:LEU368 3.3 22.4 1.0
CB C:ASN423 3.3 23.1 1.0
C10 C:NTD502 3.6 26.4 1.0
CD1 C:LEU427 3.8 24.4 1.0
C13 C:NTD502 4.1 24.2 1.0
OE1 C:GLN379 4.1 21.2 1.0
CG C:ASN423 4.2 24.2 1.0
CE2 C:PHE381 4.2 24.7 1.0
C C:ASN423 4.3 23.2 1.0
O C:GLY420 4.4 23.2 1.0
CA C:ASN423 4.4 22.4 1.0
N C:PHE424 4.4 23.6 1.0
ND2 C:ASN423 4.5 25.9 1.0
CG C:LEU368 4.6 22.1 1.0
O C:ASN423 4.7 23.8 1.0
C9 C:NTD502 4.7 27.5 1.0
CD1 C:PHE424 4.8 24.7 1.0
CE1 C:PHE424 4.8 23.9 1.0
CZ C:PHE381 4.9 24.0 1.0
C8 C:NTD502 4.9 24.6 1.0
CD2 C:PHE381 5.0 23.7 1.0
OD1 C:ASN423 5.0 22.6 1.0
CD C:GLN379 5.0 20.7 1.0

Fluorine binding site 10 out of 12 in 6j63

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Fluorine binding site 10 out of 12 in the Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Arabidopsis Thaliana Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:18.7
occ:1.00
 F2 D:NTD502 0.0 18.7 1.0
C14 D:NTD502 1.4 20.1 1.0
F1 D:NTD502 2.2 17.8 1.0
F3 D:NTD502 2.2 21.0 1.0
C11 D:NTD502 2.4 21.3 1.0
C10 D:NTD502 2.7 24.7 1.0
C12 D:NTD502 3.6 21.8 1.0
CZ D:PHE424 4.0 26.5 1.0
C9 D:NTD502 4.1 27.4 1.0
CE2 D:PHE424 4.1 26.3 1.0
CE1 D:PHE424 4.3 25.0 1.0
CD2 D:PHE424 4.4 25.8 1.0
CD1 D:PHE424 4.6 24.9 1.0
CG D:PHE424 4.7 25.4 1.0
C13 D:NTD502 4.7 22.0 1.0
CD2 D:LEU427 4.8 30.5 1.0
C8 D:NTD502 4.9 24.2 1.0
N D:NTD502 4.9 31.8 1.0
ON2 D:NTD502 4.9 33.0 1.0
CE1 D:PHE381 5.0 23.6 1.0

Reference:

H.Y.Lin, J.F.Yang, D.W.Wang, G.F.Hao, J.Q.Dong, Y.X.Wang, W.C.Yang, J.W.Wu, C.G.Zhan, G.F.Yang. Molecular Insights Into the Mechanism of 4-Hydroxyphenylpyruvate Dioxygenase Inhibition: Enzyme Kinetics, X-Ray Crystallography and Computational Simulations. Febs J. V. 286 975 2019.
ISSN: ISSN 1742-4658
PubMed: 30632699
DOI: 10.1111/FEBS.14747
Page generated: Thu Aug 1 21:28:32 2024

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