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Fluorine in PDB 6evc: Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid

Enzymatic activity of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid

All present enzymatic activity of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid:
4.1.1.102;

Protein crystallography data

The structure of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid, PDB code: 6evc was solved by S.S.Bailey, L.David, K.A.P.Payne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.05 / 1.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.240, 64.330, 88.100, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.8

Other elements in 6evc:

The structure of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid also contains other interesting chemical elements:

Potassium (K) 2 atoms
Manganese (Mn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid (pdb code 6evc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid, PDB code: 6evc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6evc

Go back to Fluorine Binding Sites List in 6evc
Fluorine binding site 1 out of 5 in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F605

b:21.8
occ:0.50
 FD1 A:F5C605 0.0 21.8 0.5
CD1 A:F5C605 1.4 18.7 0.5
CE1 A:F5C605 2.3 19.9 0.5
CG A:F5C605 2.4 20.1 0.5
FE1 A:F5C605 2.6 20.7 0.5
CD2 A:LEU185 2.9 11.9 0.5
N3 A:4LU601 3.1 18.0 1.0
CB A:F5C605 3.2 21.0 0.5
C2 A:4LU601 3.2 14.2 1.0
CD1 A:ILE187 3.3 15.0 1.0
CA A:F5C605 3.4 24.3 0.5
O2 A:4LU601 3.5 12.5 1.0
CZ A:F5C605 3.6 19.2 0.5
CD2 A:F5C605 3.6 18.0 0.5
CD1 A:LEU185 3.7 15.7 0.5
CD2 A:LEU439 3.7 16.7 0.5
C4 A:4LU601 3.8 8.6 1.0
CG A:LEU185 3.8 11.5 0.5
CD1 A:LEU439 3.9 13.0 0.5
CG1 A:ILE187 4.0 12.0 1.0
CE2 A:F5C605 4.1 18.7 0.5
N1 A:4LU601 4.1 12.1 1.0
O4 A:4LU601 4.2 18.5 1.0
CG A:LEU439 4.3 16.5 0.5
CE1 A:PHE437 4.4 11.6 1.0
CD2 A:LEU439 4.4 15.7 0.5
C4A A:4LU601 4.5 9.8 1.0
CG A:LEU439 4.6 16.1 0.5
FD2 A:F5C605 4.6 18.1 0.5
FZ A:F5C605 4.6 18.7 0.5
C10 A:4LU601 4.6 9.2 1.0
O A:HOH894 4.7 12.8 1.0
CD1 A:LEU439 4.7 19.1 0.5
CB A:LEU185 4.7 12.7 0.5
CD1 A:LEU185 4.8 12.0 0.5
OH A:TYR394 4.9 13.1 1.0
CZ A:PHE437 4.9 10.2 1.0
CG A:LEU185 4.9 15.8 0.5
C A:F5C605 4.9 23.0 0.5
CB A:LEU185 5.0 11.0 0.5

Fluorine binding site 2 out of 5 in 6evc

Go back to Fluorine Binding Sites List in 6evc
Fluorine binding site 2 out of 5 in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F605

b:18.1
occ:0.50
 FD2 A:F5C605 0.0 18.1 0.5
CD2 A:F5C605 1.2 18.0 0.5
CG A:F5C605 2.1 20.1 0.5
CB A:F5C605 2.2 21.0 0.5
CE2 A:F5C605 2.2 18.7 0.5
FE2 A:F5C605 2.7 18.9 0.5
CD1 A:ILE327 3.2 8.4 1.0
SD A:MET283 3.4 9.8 1.0
CD1 A:F5C605 3.4 18.7 0.5
CZ A:F5C605 3.5 19.2 0.5
CA A:F5C605 3.5 24.3 0.5
C10 A:4LU601 3.5 9.2 1.0
N10 A:4LU601 3.6 8.6 1.0
C4A A:4LU601 3.8 9.8 1.0
OXT A:F5C605 3.8 14.6 0.5
N5 A:4LU601 3.8 10.2 1.0
C1' A:4LU601 3.9 8.1 1.0
CE1 A:F5C605 3.9 19.9 0.5
C A:F5C605 4.0 23.0 0.5
N1 A:4LU601 4.0 12.1 1.0
C9A A:4LU601 4.0 7.4 1.0
CZ A:PHE437 4.1 10.2 1.0
C5A A:4LU601 4.2 7.8 1.0
C1 A:4LU601 4.4 15.2 1.0
C4 A:4LU601 4.5 8.6 1.0
CG1 A:ILE327 4.5 7.9 1.0
FZ A:F5C605 4.5 18.7 0.5
CG2 A:ILE327 4.6 9.2 1.0
FD1 A:F5C605 4.6 21.8 0.5
CG A:MET283 4.6 8.7 1.0
C2 A:4LU601 4.7 14.2 1.0
CE A:MET283 4.7 10.8 1.0
N3 A:4LU601 4.9 18.0 1.0
C9 A:4LU601 4.9 6.9 1.0
CE2 A:PHE437 5.0 8.3 1.0
CE1 A:PHE437 5.0 11.6 1.0
C3 A:4LU601 5.0 10.7 1.0

Fluorine binding site 3 out of 5 in 6evc

Go back to Fluorine Binding Sites List in 6evc
Fluorine binding site 3 out of 5 in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F605

b:20.7
occ:0.50
 FE1 A:F5C605 0.0 20.7 0.5
CE1 A:F5C605 1.4 19.9 0.5
CD1 A:F5C605 2.4 18.7 0.5
CZ A:F5C605 2.4 19.2 0.5
FD1 A:F5C605 2.6 21.8 0.5
FZ A:F5C605 2.8 18.7 0.5
CE2 A:TYR394 3.2 12.2 1.0
O2 A:4LU601 3.2 12.5 1.0
CD1 A:ILE187 3.3 15.0 1.0
OH A:TYR394 3.4 13.1 1.0
NE2 A:GLN190 3.4 9.1 1.0
C2 A:4LU601 3.5 14.2 1.0
CG A:GLN190 3.5 7.8 1.0
CG1 A:ILE187 3.5 12.0 1.0
CD A:GLN190 3.6 7.8 1.0
CG A:F5C605 3.6 20.1 0.5
CE2 A:F5C605 3.6 18.7 0.5
CZ A:TYR394 3.8 11.2 1.0
CE1 A:PHE437 4.1 11.6 1.0
N1 A:4LU601 4.1 12.1 1.0
CD2 A:F5C605 4.1 18.0 0.5
CD2 A:TYR394 4.3 10.4 1.0
N3 A:4LU601 4.3 18.0 1.0
OE1 A:GLN190 4.4 9.0 1.0
O A:HOH894 4.6 12.8 1.0
FE2 A:F5C605 4.7 18.9 0.5
CZ A:PHE437 4.8 10.2 1.0
CD1 A:PHE437 4.9 10.0 1.0
CB A:F5C605 4.9 21.0 0.5
CB A:GLN190 4.9 8.0 1.0

Fluorine binding site 4 out of 5 in 6evc

Go back to Fluorine Binding Sites List in 6evc
Fluorine binding site 4 out of 5 in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F605

b:18.9
occ:0.50
 FE2 A:F5C605 0.0 18.9 0.5
CE2 A:F5C605 1.3 18.7 0.5
CZ A:F5C605 2.3 19.2 0.5
CD2 A:F5C605 2.3 18.0 0.5
FZ A:F5C605 2.7 18.7 0.5
FD2 A:F5C605 2.7 18.1 0.5
CG2 A:THR395 3.3 9.6 1.0
C1' A:4LU601 3.3 8.1 1.0
CG2 A:ILE327 3.3 9.2 1.0
CE1 A:F5C605 3.6 19.9 0.5
CG A:F5C605 3.6 20.1 0.5
O3' A:4LU601 3.7 7.8 1.0
O A:HOH829 3.8 11.0 1.0
CD1 A:ILE327 4.0 8.4 1.0
CD1 A:F5C605 4.0 18.7 0.5
N10 A:4LU601 4.0 8.6 1.0
CZ A:PHE437 4.1 10.2 1.0
N1 A:4LU601 4.1 12.1 1.0
C10 A:4LU601 4.3 9.2 1.0
C2' A:4LU601 4.4 7.1 1.0
C3' A:4LU601 4.4 7.2 1.0
CB A:F5C605 4.4 21.0 0.5
CG1 A:ILE327 4.5 7.9 1.0
CB A:ILE327 4.5 8.0 1.0
CB A:THR395 4.6 8.1 1.0
NE2 A:GLN190 4.6 9.1 1.0
SD A:MET283 4.6 9.8 1.0
FE1 A:F5C605 4.7 20.7 0.5
CE2 A:PHE437 4.7 8.3 1.0
CE1 A:PHE437 4.8 11.6 1.0
C2 A:4LU601 5.0 14.2 1.0
C9A A:4LU601 5.0 7.4 1.0

Fluorine binding site 5 out of 5 in 6evc

Go back to Fluorine Binding Sites List in 6evc
Fluorine binding site 5 out of 5 in the Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of E282Q A. Niger FDC1 in Complex with Pentafluoro-Cinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F605

b:18.7
occ:0.50
 FZ A:F5C605 0.0 18.7 0.5
CZ A:F5C605 1.2 19.2 0.5
CE1 A:F5C605 2.3 19.9 0.5
CE2 A:F5C605 2.3 18.7 0.5
FE2 A:F5C605 2.7 18.9 0.5
FE1 A:F5C605 2.8 20.7 0.5
NE2 A:GLN190 2.8 9.1 1.0
CE2 A:TYR394 3.1 12.2 1.0
CD2 A:TYR394 3.3 10.4 1.0
CD A:GLN190 3.4 7.8 1.0
O3' A:4LU601 3.5 7.8 1.0
CG2 A:THR395 3.5 9.6 1.0
CD1 A:F5C605 3.5 18.7 0.5
CD2 A:F5C605 3.6 18.0 0.5
OE1 A:GLN190 3.7 9.0 1.0
CG A:F5C605 4.0 20.1 0.5
N1 A:4LU601 4.1 12.1 1.0
CE1 A:PHE437 4.3 11.6 1.0
CG A:GLN190 4.3 7.8 1.0
O A:HOH829 4.3 11.0 1.0
C2 A:4LU601 4.3 14.2 1.0
CZ A:TYR394 4.4 11.2 1.0
O2 A:4LU601 4.4 12.5 1.0
CZ A:PHE437 4.4 10.2 1.0
O A:HOH798 4.4 9.0 1.0
C1' A:4LU601 4.5 8.1 1.0
FD2 A:F5C605 4.5 18.1 0.5
FD1 A:F5C605 4.6 21.8 0.5
CG A:TYR394 4.7 9.9 1.0
C3' A:4LU601 4.8 7.2 1.0
OH A:TYR394 4.8 13.1 1.0
C2' A:4LU601 4.9 7.1 1.0
O A:HOH973 5.0 11.1 1.0
C10 A:4LU601 5.0 9.2 1.0

Reference:

S.S.Bailey, K.A.P.Payne, K.Fisher, S.A.Marshall, M.J.Cliff, R.Spiess, D.A.Parker, S.E.J.Rigby, D.Leys. The Role of Conserved Residues in Fdc Decarboxylase in Prenylated Flavin Mononucleotide Oxidative Maturation, Cofactor Isomerization, and Catalysis. J. Biol. Chem. V. 293 2272 2018.
ISSN: ESSN 1083-351X
PubMed: 29259125
DOI: 10.1074/JBC.RA117.000881
Page generated: Thu Aug 1 19:47:28 2024

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