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Fluorine in PDB 4za8: Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid

Enzymatic activity of Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid

All present enzymatic activity of Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid:
4.1.1.61;

Protein crystallography data

The structure of Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid, PDB code: 4za8 was solved by K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.81 / 1.06
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.010, 63.930, 87.840, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16.6

Other elements in 4za8:

The structure of Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic 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 Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid (pdb code 4za8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid, PDB code: 4za8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4za8

Go back to Fluorine Binding Sites List in 4za8
Fluorine binding site 1 out of 5 in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid


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 A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:15.4
occ:0.60
 FD1 A:F5C606 0.0 15.4 0.6
CD1 A:F5C606 1.3 15.3 0.6
CE1 A:F5C606 2.2 13.7 0.6
CG A:F5C606 2.3 14.3 0.6
FE1 A:F5C606 2.6 18.2 0.6
CB A:F5C606 2.7 14.9 0.6
CD2 A:LEU185 2.9 19.8 0.5
N3 A:4LU601 3.2 15.4 0.5
N1 A:FZZ602 3.3 10.9 0.5
C2 A:4LU601 3.3 12.0 0.5
CD2 A:F5C606 3.4 11.4 0.6
CD1 A:ILE187 3.5 14.4 1.0
CZ A:F5C606 3.5 17.0 0.6
C2 A:FZZ602 3.5 12.2 0.5
O2 A:4LU601 3.5 13.2 0.5
C1 A:FZZ602 3.6 15.6 0.5
CD2 A:LEU439 3.6 24.1 0.5
C4 A:4LU601 3.7 10.4 0.5
CD1 A:LEU185 3.7 11.3 0.5
O2 A:FZZ602 3.9 9.9 0.5
CD1 A:LEU439 3.9 15.6 0.5
CE2 A:F5C606 3.9 12.6 0.6
CG A:LEU185 4.0 13.5 0.5
O1 A:FZZ602 4.0 14.3 0.5
N2 A:FZZ602 4.1 10.6 0.5
N1 A:4LU601 4.1 12.3 0.5
O4 A:4LU601 4.1 16.4 0.5
C3 A:FZZ602 4.1 11.2 0.5
CG1 A:ILE187 4.2 11.5 1.0
CA A:F5C606 4.2 15.8 0.6
CG A:LEU439 4.3 18.8 0.5
C4A A:4LU601 4.3 8.7 0.5
CE1 A:PHE437 4.3 11.4 1.0
C17 A:FZZ602 4.3 10.5 0.5
CD2 A:LEU439 4.4 22.2 0.5
CD1 A:LEU439 4.5 23.1 0.5
CG A:LEU439 4.5 15.6 0.5
C10 A:4LU601 4.6 7.7 0.5
FD2 A:F5C606 4.6 16.3 0.6
FZ A:F5C606 4.6 19.8 0.6
N3 A:FZZ602 4.7 13.0 0.5
CZ A:PHE437 4.8 10.9 1.0
CB A:LEU185 4.8 12.1 0.5
OH A:TYR394 4.9 13.5 1.0
O A:HOH814 4.9 12.7 1.0
CG A:LEU185 5.0 14.1 0.5

Fluorine binding site 2 out of 5 in 4za8

Go back to Fluorine Binding Sites List in 4za8
Fluorine binding site 2 out of 5 in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid


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 A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:16.3
occ:0.60
 FD2 A:F5C606 0.0 16.3 0.6
CD2 A:F5C606 1.3 11.4 0.6
CE2 A:F5C606 2.3 12.6 0.6
CG A:F5C606 2.3 14.3 0.6
CA A:F5C606 2.6 15.8 0.6
FE2 A:F5C606 2.8 19.1 0.6
CB A:F5C606 2.9 14.9 0.6
CD1 A:ILE327 3.0 9.9 1.0
SD A:MET283 3.3 9.5 1.0
N4 A:FZZ602 3.5 9.2 0.5
CD1 A:F5C606 3.5 15.3 0.6
CZ A:F5C606 3.6 17.0 0.6
N10 A:4LU601 3.6 8.1 0.5
C10 A:4LU601 3.6 7.7 0.5
N5 A:4LU601 3.7 7.2 0.5
C17 A:FZZ602 3.7 10.5 0.5
C18 A:FZZ602 3.8 9.9 0.5
C4A A:4LU601 3.8 8.7 0.5
C1' A:4LU601 3.9 7.6 0.5
C9A A:4LU601 3.9 7.4 0.5
C16 A:FZZ602 4.0 7.6 0.5
CE1 A:F5C606 4.0 13.7 0.6
C5A A:4LU601 4.0 8.0 0.5
C A:F5C606 4.1 17.0 0.6
N3 A:FZZ602 4.1 13.0 0.5
C4 A:FZZ602 4.1 14.8 0.5
C15 A:FZZ602 4.1 10.0 0.5
CZ A:PHE437 4.2 10.9 1.0
N1 A:4LU601 4.2 12.3 0.5
C3 A:FZZ602 4.2 11.2 0.5
CG1 A:ILE327 4.2 9.5 1.0
C1 A:4LU601 4.3 9.5 0.5
CG2 A:ILE327 4.4 9.8 1.0
N2 A:FZZ602 4.4 10.6 0.5
OXT A:F5C606 4.5 14.1 0.6
CE A:MET283 4.5 11.2 1.0
CG A:MET283 4.5 9.3 1.0
FD1 A:F5C606 4.6 15.4 0.6
C4 A:4LU601 4.7 10.4 0.5
FZ A:F5C606 4.7 19.8 0.6
C14 A:FZZ602 4.7 9.5 0.5
C5 A:FZZ602 4.7 13.0 0.5
CB A:ILE327 4.8 8.1 1.0
CD2 A:LEU439 4.8 24.1 0.5
C9 A:4LU601 4.9 7.2 0.5
C2 A:4LU601 4.9 12.0 0.5
C6 A:4LU601 5.0 7.9 0.5

Fluorine binding site 3 out of 5 in 4za8

Go back to Fluorine Binding Sites List in 4za8
Fluorine binding site 3 out of 5 in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid


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 A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:18.2
occ:0.60
 FE1 A:F5C606 0.0 18.2 0.6
CE1 A:F5C606 1.4 13.7 0.6
CD1 A:F5C606 2.4 15.3 0.6
CZ A:F5C606 2.4 17.0 0.6
FD1 A:F5C606 2.6 15.4 0.6
FZ A:F5C606 2.8 19.8 0.6
CE2 A:TYR394 3.1 12.9 1.0
O2 A:4LU601 3.2 13.2 0.5
NE2 A:GLN190 3.4 10.3 1.0
OH A:TYR394 3.4 13.5 1.0
O2 A:FZZ602 3.4 9.9 0.5
CD1 A:ILE187 3.4 14.4 1.0
CG A:GLN190 3.5 8.2 1.0
CD A:GLN190 3.6 8.4 1.0
CG1 A:ILE187 3.6 11.5 1.0
C2 A:4LU601 3.6 12.0 0.5
CE2 A:F5C606 3.6 12.6 0.6
CZ A:TYR394 3.7 12.9 1.0
CG A:F5C606 3.7 14.3 0.6
C2 A:FZZ602 3.7 12.2 0.5
CD2 A:F5C606 4.1 11.4 0.6
CE1 A:PHE437 4.1 11.4 1.0
N1 A:4LU601 4.1 12.3 0.5
CD2 A:TYR394 4.2 11.4 1.0
N2 A:FZZ602 4.2 10.6 0.5
N1 A:FZZ602 4.3 10.9 0.5
N3 A:4LU601 4.3 15.4 0.5
OE1 A:GLN190 4.4 9.9 1.0
FE2 A:F5C606 4.6 19.1 0.6
O A:HOH814 4.7 12.7 1.0
CB A:F5C606 4.8 14.9 0.6
CD1 A:PHE437 4.9 10.1 1.0
CZ A:PHE437 4.9 10.9 1.0
CB A:GLN190 4.9 8.0 1.0

Fluorine binding site 4 out of 5 in 4za8

Go back to Fluorine Binding Sites List in 4za8
Fluorine binding site 4 out of 5 in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid


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 A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:19.1
occ:0.60
 FE2 A:F5C606 0.0 19.1 0.6
CE2 A:F5C606 1.3 12.6 0.6
CZ A:F5C606 2.2 17.0 0.6
CD2 A:F5C606 2.4 11.4 0.6
FZ A:F5C606 2.6 19.8 0.6
FD2 A:F5C606 2.8 16.3 0.6
CG2 A:THR395 3.1 9.9 1.0
CG2 A:ILE327 3.4 9.8 1.0
C1' A:4LU601 3.4 7.6 0.5
CE1 A:F5C606 3.5 13.7 0.6
C18 A:FZZ602 3.5 9.9 0.5
O4 A:FZZ602 3.5 8.5 0.5
O3' A:4LU601 3.6 9.0 0.5
CG A:F5C606 3.6 14.3 0.6
O A:HOH727 3.7 12.2 1.0
CD1 A:F5C606 4.0 15.3 0.6
CZ A:PHE437 4.0 10.9 1.0
N10 A:4LU601 4.1 8.1 0.5
CD1 A:ILE327 4.1 9.9 1.0
N4 A:FZZ602 4.2 9.2 0.5
N1 A:4LU601 4.2 12.3 0.5
C10 A:4LU601 4.4 7.7 0.5
C20 A:FZZ602 4.4 8.3 0.5
CB A:THR395 4.4 8.5 1.0
C2' A:4LU601 4.5 8.8 0.5
C3' A:4LU601 4.5 8.3 0.5
C19 A:FZZ602 4.5 10.1 0.5
NE2 A:GLN190 4.5 10.3 1.0
CG1 A:ILE327 4.5 9.5 1.0
CB A:ILE327 4.5 8.1 1.0
N2 A:FZZ602 4.6 10.6 0.5
C17 A:FZZ602 4.6 10.5 0.5
SD A:MET283 4.6 9.5 1.0
FE1 A:F5C606 4.6 18.2 0.6
CE1 A:PHE437 4.6 11.4 1.0
CE2 A:PHE437 4.7 10.1 1.0
CB A:F5C606 5.0 14.9 0.6
C9A A:4LU601 5.0 7.4 0.5
OG1 A:THR395 5.0 8.4 1.0

Fluorine binding site 5 out of 5 in 4za8

Go back to Fluorine Binding Sites List in 4za8
Fluorine binding site 5 out of 5 in the Crystal Structure of A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid


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 A Niger FDC1 in Complex with Penta-Fluorocinnamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F606

b:19.8
occ:0.60
 FZ A:F5C606 0.0 19.8 0.6
CZ A:F5C606 1.4 17.0 0.6
CE1 A:F5C606 2.4 13.7 0.6
CE2 A:F5C606 2.4 12.6 0.6
FE2 A:F5C606 2.6 19.1 0.6
FE1 A:F5C606 2.8 18.2 0.6
NE2 A:GLN190 2.9 10.3 1.0
CE2 A:TYR394 3.0 12.9 1.0
CD2 A:TYR394 3.2 11.4 1.0
CG2 A:THR395 3.4 9.9 1.0
CD A:GLN190 3.4 8.4 1.0
O4 A:FZZ602 3.4 8.5 0.5
O3' A:4LU601 3.5 9.0 0.5
CD1 A:F5C606 3.6 15.3 0.6
CD2 A:F5C606 3.7 11.4 0.6
OE1 A:GLN190 3.7 9.9 1.0
O A:HOH727 4.2 12.2 1.0
CG A:F5C606 4.2 14.3 0.6
CE1 A:PHE437 4.2 11.4 1.0
N1 A:4LU601 4.3 12.3 0.5
CZ A:TYR394 4.3 12.9 1.0
CG A:GLN190 4.3 8.2 1.0
O A:HOH741 4.4 9.6 1.0
CZ A:PHE437 4.4 10.9 1.0
CG A:TYR394 4.5 10.6 1.0
N2 A:FZZ602 4.5 10.6 0.5
O2 A:4LU601 4.6 13.2 0.5
C18 A:FZZ602 4.6 9.9 0.5
C1' A:4LU601 4.6 7.6 0.5
FD1 A:F5C606 4.6 15.4 0.6
C2 A:4LU601 4.6 12.0 0.5
O2 A:FZZ602 4.7 9.9 0.5
FD2 A:F5C606 4.7 16.3 0.6
C20 A:FZZ602 4.7 8.3 0.5
OH A:TYR394 4.8 13.5 1.0
O A:HOH906 4.8 12.2 1.0
C3' A:4LU601 4.8 8.3 0.5
C2 A:FZZ602 4.8 12.2 0.5
CB A:THR395 4.9 8.5 1.0
C2' A:4LU601 5.0 8.8 0.5
CD1 A:PHE437 5.0 10.1 1.0

Reference:

K.A.Payne, M.D.White, K.Fisher, B.Khara, S.S.Bailey, D.Parker, N.J.Rattray, D.K.Trivedi, R.Goodacre, R.Beveridge, P.Barran, S.E.Rigby, N.S.Scrutton, S.Hay, D.Leys. New Cofactor Supports Alpha , Beta-Unsaturated Acid Decarboxylation Via 1,3-Dipolar Cycloaddition. Nature V. 522 502 2015.
ISSN: ESSN 1476-4687
PubMed: 26083754
DOI: 10.1038/NATURE14560
Page generated: Sun Dec 13 12:16:36 2020

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