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Fluorine in PDB 6r3i: Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)

Enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)

All present enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2):
4.1.1.102;

Protein crystallography data

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2), PDB code: 6r3i was solved by S.S.Bailey, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.73 / 1.14
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.196, 64.079, 87.508, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 14.6

Other elements in 6r3i:

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) 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 Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) (pdb code 6r3i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2), PDB code: 6r3i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6r3i

Go back to Fluorine Binding Sites List in 6r3i
Fluorine binding site 1 out of 5 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:13.5
occ:1.00
 F49 A:JRN604 0.0 13.5 1.0
C39 A:JRN604 1.3 11.7 1.0
C40 A:JRN604 2.3 11.7 1.0
C38 A:JRN604 2.4 12.6 1.0
F48 A:JRN604 2.6 13.8 1.0
C37 A:JRN604 2.8 14.8 1.0
N02 A:JRN604 3.1 7.2 1.0
CD2 A:LEU185 3.2 10.8 0.5
C01 A:JRN604 3.2 7.4 1.0
CD1 A:LEU439 3.3 10.6 0.5
CD2 A:LEU439 3.4 17.2 0.5
C03 A:JRN604 3.5 7.1 1.0
C42 A:JRN604 3.5 11.7 1.0
O17 A:JRN604 3.6 8.2 1.0
C46 A:JRN604 3.7 11.2 1.0
CD1 A:LEU185 3.7 11.4 0.5
CD1 A:ILE187 3.8 12.5 1.0
N06 A:JRN604 3.9 6.9 1.0
O24 A:JRN604 4.0 7.6 1.0
C41 A:JRN604 4.0 14.0 1.0
C04 A:JRN604 4.1 7.4 1.0
C36 A:JRN604 4.2 14.9 1.0
CG A:LEU185 4.3 8.9 0.5
C05 A:JRN604 4.3 6.4 1.0
CG1 A:ILE187 4.3 10.7 1.0
CD1 A:LEU439 4.4 16.6 0.5
CE1 A:PHE437 4.5 10.4 1.0
CG A:LEU439 4.5 9.7 0.5
CG A:LEU439 4.5 15.4 0.5
F44 A:JRN604 4.7 18.8 1.0
F47 A:JRN604 4.7 18.0 1.0
CZ A:PHE437 4.8 9.8 1.0
O A:HOH841 4.9 11.1 1.0
CB A:LEU185 4.9 9.9 0.5
C19 A:JRN604 5.0 8.5 1.0
CG A:LEU185 5.0 12.8 0.5

Fluorine binding site 2 out of 5 in 6r3i

Go back to Fluorine Binding Sites List in 6r3i
Fluorine binding site 2 out of 5 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:13.8
occ:1.00
 F48 A:JRN604 0.0 13.8 1.0
C40 A:JRN604 1.4 11.7 1.0
C39 A:JRN604 2.3 11.7 1.0
C46 A:JRN604 2.4 11.2 1.0
F49 A:JRN604 2.6 13.5 1.0
F47 A:JRN604 2.7 18.0 1.0
CE2 A:TYR394 3.3 11.4 1.0
O17 A:JRN604 3.3 8.2 1.0
NE2 A:GLN190 3.4 7.8 1.0
CD1 A:ILE187 3.5 12.5 1.0
C41 A:JRN604 3.5 14.0 1.0
CG A:GLN190 3.6 7.2 1.0
CD A:GLN190 3.7 7.0 1.0
C38 A:JRN604 3.7 12.6 1.0
CG1 A:ILE187 3.7 10.7 1.0
OH A:TYR394 3.7 12.3 1.0
C01 A:JRN604 3.7 7.4 1.0
C42 A:JRN604 4.0 11.7 1.0
CE1 A:PHE437 4.0 10.4 1.0
CZ A:TYR394 4.1 10.6 1.0
N06 A:JRN604 4.2 6.9 1.0
CD2 A:TYR394 4.3 9.7 1.0
N02 A:JRN604 4.4 7.2 1.0
OE1 A:GLN190 4.5 8.2 1.0
F45 A:JRN604 4.6 17.2 1.0
CZ A:PHE437 4.7 9.8 1.0
C37 A:JRN604 4.8 14.8 1.0
O A:HOH841 4.8 11.1 1.0
CD1 A:PHE437 4.8 9.5 1.0
CD1 A:LEU439 5.0 10.6 0.5

Fluorine binding site 3 out of 5 in 6r3i

Go back to Fluorine Binding Sites List in 6r3i
Fluorine binding site 3 out of 5 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:18.0
occ:1.00
 F47 A:JRN604 0.0 18.0 1.0
C46 A:JRN604 1.3 11.2 1.0
C41 A:JRN604 2.3 14.0 1.0
C40 A:JRN604 2.4 11.7 1.0
F45 A:JRN604 2.7 17.2 1.0
F48 A:JRN604 2.7 13.8 1.0
NE2 A:GLN190 3.0 7.8 1.0
CE2 A:TYR394 3.1 11.4 1.0
CD2 A:TYR394 3.2 9.7 1.0
CG2 A:THR395 3.3 11.0 1.0
CD A:GLN190 3.4 7.0 1.0
C42 A:JRN604 3.6 11.7 1.0
C39 A:JRN604 3.6 11.7 1.0
OE1 A:GLN190 3.7 8.2 1.0
O34 A:JRN604 3.7 6.8 1.0
C38 A:JRN604 4.2 12.6 1.0
O A:HOH783 4.2 10.8 1.0
CE1 A:PHE437 4.3 10.4 1.0
CG A:GLN190 4.4 7.2 1.0
O A:HOH742 4.4 8.8 1.0
CZ A:TYR394 4.4 10.6 1.0
CZ A:PHE437 4.5 9.8 1.0
CG A:TYR394 4.5 8.7 1.0
F44 A:JRN604 4.6 18.8 1.0
N06 A:JRN604 4.6 6.9 1.0
O A:HOH916 4.6 11.9 1.0
F49 A:JRN604 4.7 13.5 1.0
O17 A:JRN604 4.8 8.2 1.0
C18 A:JRN604 4.8 6.6 1.0
CB A:THR395 4.9 8.9 1.0
OH A:TYR394 4.9 12.3 1.0
C01 A:JRN604 4.9 7.4 1.0
CD1 A:PHE437 5.0 9.5 1.0

Fluorine binding site 4 out of 5 in 6r3i

Go back to Fluorine Binding Sites List in 6r3i
Fluorine binding site 4 out of 5 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:17.2
occ:1.00
 F45 A:JRN604 0.0 17.2 1.0
C41 A:JRN604 1.3 14.0 1.0
C46 A:JRN604 2.2 11.2 1.0
C42 A:JRN604 2.3 11.7 1.0
F44 A:JRN604 2.6 18.8 1.0
F47 A:JRN604 2.7 18.0 1.0
CG2 A:THR395 3.0 11.0 1.0
CG2 A:ILE327 3.3 10.3 1.0
O A:HOH783 3.5 10.8 1.0
C40 A:JRN604 3.5 11.7 1.0
C38 A:JRN604 3.6 12.6 1.0
O34 A:JRN604 3.7 6.8 1.0
C18 A:JRN604 3.7 6.6 1.0
C39 A:JRN604 4.0 11.7 1.0
CB A:THR395 4.3 8.9 1.0
CZ A:PHE437 4.3 9.8 1.0
CD1 A:ILE327 4.5 9.4 1.0
CE A:MET283 4.5 12.8 0.3
N10 A:JRN604 4.5 6.8 1.0
C26 A:JRN604 4.5 6.1 1.0
CB A:ILE327 4.6 8.9 1.0
NE2 A:GLN190 4.6 7.8 1.0
F48 A:JRN604 4.6 13.8 1.0
C25 A:JRN604 4.7 6.1 1.0
N06 A:JRN604 4.7 6.9 1.0
OG1 A:THR395 4.7 8.9 1.0
C37 A:JRN604 4.8 14.8 1.0
C05 A:JRN604 4.8 6.4 1.0
CE2 A:PHE437 4.8 8.7 1.0
CG1 A:ILE327 4.8 8.5 1.0
CE A:MET283 4.9 24.3 0.7
SD A:MET283 4.9 7.7 0.3
CE1 A:PHE437 4.9 10.4 1.0

Fluorine binding site 5 out of 5 in 6r3i

Go back to Fluorine Binding Sites List in 6r3i
Fluorine binding site 5 out of 5 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) E282Q Variant in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Pentafluorocinnamic Acid (INT2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F604

b:18.8
occ:1.00
 F44 A:JRN604 0.0 18.8 1.0
C42 A:JRN604 1.3 11.7 1.0
C41 A:JRN604 2.2 14.0 1.0
C38 A:JRN604 2.3 12.6 1.0
F45 A:JRN604 2.6 17.2 1.0
C37 A:JRN604 2.8 14.8 1.0
C36 A:JRN604 2.9 14.9 1.0
CD1 A:ILE327 3.0 9.4 1.0
C46 A:JRN604 3.4 11.2 1.0
SD A:MET283 3.5 7.7 0.3
C39 A:JRN604 3.6 11.7 1.0
CE A:MET283 3.6 24.3 0.7
N10 A:JRN604 3.7 6.8 1.0
CE A:MET283 3.8 12.8 0.3
C18 A:JRN604 3.8 6.6 1.0
CG2 A:ILE327 3.9 10.3 1.0
C40 A:JRN604 3.9 11.7 1.0
SD A:MET283 4.0 38.8 0.7
C05 A:JRN604 4.0 6.4 1.0
C09 A:JRN604 4.2 6.4 1.0
CG1 A:ILE327 4.2 8.5 1.0
CZ A:PHE437 4.3 9.8 1.0
C19 A:JRN604 4.3 8.5 1.0
C04 A:JRN604 4.3 7.4 1.0
N07 A:JRN604 4.3 7.4 1.0
C08 A:JRN604 4.4 6.5 1.0
N06 A:JRN604 4.5 6.9 1.0
CB A:ILE327 4.5 8.9 1.0
F47 A:JRN604 4.6 18.0 1.0
F49 A:JRN604 4.7 13.5 1.0
CB A:GLN282 4.7 14.4 0.3
CG A:MET283 4.8 28.5 0.7
CG A:GLN282 4.9 14.7 0.3
C14 A:JRN604 4.9 6.5 1.0
CE2 A:PHE437 5.0 8.7 1.0

Reference:

S.S.Bailey, K.A.P.Payne, A.Saaret, S.A.Marshall, I.Gostimskaya, I.Kosov, K.Fisher, S.Hay, D.Leys. Atomic Description of An Enzyme Reaction Dependent on Reversible 1,3-Dipolar Cycloaddition To Be Published.
Page generated: Tue Jul 15 15:13:27 2025

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