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Fluorine in PDB 2ycn: Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine

Enzymatic activity of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine

All present enzymatic activity of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine:
4.1.99.2;

Protein crystallography data

The structure of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine, PDB code: 2ycn was solved by D.Milic, T.V.Demidkina, N.G.Faleev, R.S.Phillips, D.Matkovic-Calogovic, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.06 / 2.04
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.635, 144.397, 59.660, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.9

Other elements in 2ycn:

The structure of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine also contains other interesting chemical elements:

Potassium (K) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine (pdb code 2ycn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine, PDB code: 2ycn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2ycn

Go back to Fluorine Binding Sites List in 2ycn
Fluorine binding site 1 out of 3 in the Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:36.9
occ:0.67
 F A:P61600 0.0 36.9 0.7
F A:P61600 0.9 29.7 0.3
CE1 A:P61600 1.3 35.5 0.7
CE1 A:P61600 1.6 27.8 0.3
CD1 A:P61600 2.3 26.6 0.3
CZ A:P61600 2.3 33.2 0.7
CD1 A:P61600 2.4 31.2 0.7
CZ A:P61600 2.7 23.6 0.3
OH A:P61600 2.7 30.7 0.7
NH2 A:ARG381 2.9 37.8 1.0
NH1 A:ARG381 3.1 35.7 1.0
SD A:MET379 3.1 37.4 1.0
OH A:P61600 3.1 23.3 0.3
CZ A:ARG381 3.2 40.8 1.0
CE A:MET379 3.3 28.9 1.0
CG A:P61600 3.6 25.2 0.3
CZ A:PHE36 3.6 44.0 1.0
CE2 A:PHE448 3.6 46.1 1.0
CE2 A:P61600 3.6 38.2 0.7
CG A:P61600 3.7 28.5 0.7
CE2 A:P61600 3.9 24.1 0.3
CD2 A:P61600 4.1 34.6 0.7
CD2 A:PHE448 4.1 49.1 1.0
NE A:ARG381 4.2 42.7 1.0
CE1 A:PHE36 4.2 33.7 1.0
CD2 A:P61600 4.2 25.9 0.3
OXT A:P61600 4.2 25.9 0.3
CE1 A:PHE449 4.3 47.7 1.0
O A:P61600 4.3 26.2 0.7
CG A:MET379 4.5 21.4 1.0
CZ A:PHE448 4.5 47.2 1.0
C A:P61600 4.5 27.6 0.3
CE2 A:PHE36 4.6 37.5 1.0
CZ A:PHE449 4.7 51.2 1.0
CB A:P61600 4.7 27.2 0.3
C A:P61600 4.7 28.3 0.7
CB A:P61600 4.8 28.7 0.7
CA A:P61600 4.8 27.2 0.3
CD1 A:PHE449 5.0 44.2 1.0

Fluorine binding site 2 out of 3 in 2ycn

Go back to Fluorine Binding Sites List in 2ycn
Fluorine binding site 2 out of 3 in the Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F600

b:29.7
occ:0.33
 F A:P61600 0.0 29.7 0.3
F A:P61600 0.9 36.9 0.7
CE1 A:P61600 1.3 27.8 0.3
CE1 A:P61600 1.6 35.5 0.7
CZ A:P61600 2.3 23.6 0.3
CD1 A:P61600 2.4 26.6 0.3
CD1 A:P61600 2.5 31.2 0.7
CZ A:P61600 2.5 33.2 0.7
OH A:P61600 2.7 23.3 0.3
OH A:P61600 2.9 30.7 0.7
CE2 A:PHE448 3.1 46.1 1.0
CZ A:PHE36 3.2 44.0 1.0
NH2 A:ARG381 3.3 37.8 1.0
CE1 A:PHE449 3.4 47.7 1.0
CE A:MET379 3.6 28.9 1.0
CE1 A:PHE36 3.6 33.7 1.0
CE2 A:P61600 3.6 24.1 0.3
CG A:P61600 3.6 25.2 0.3
CD2 A:PHE448 3.7 49.1 1.0
SD A:MET379 3.7 37.4 1.0
CE2 A:P61600 3.7 38.2 0.7
CG A:P61600 3.7 28.5 0.7
CZ A:ARG381 3.8 40.8 1.0
NH1 A:ARG381 3.9 35.7 1.0
CZ A:PHE449 3.9 51.2 1.0
CD1 A:PHE449 4.1 44.2 1.0
CZ A:PHE448 4.1 47.2 1.0
CD2 A:P61600 4.1 25.9 0.3
CD2 A:P61600 4.2 34.6 0.7
CE2 A:PHE36 4.3 37.5 1.0
CZ B:PHE71 4.6 33.0 1.0
CE2 B:PHE71 4.7 37.7 1.0
OXT A:P61600 4.7 25.9 0.3
CG A:MET379 4.8 21.4 1.0
NE A:ARG381 4.8 42.7 1.0
O A:P61600 4.9 26.2 0.7
CB A:P61600 4.9 27.2 0.3
CE2 A:PHE449 4.9 50.4 1.0
CD1 A:PHE36 4.9 33.5 1.0
CB A:P61600 5.0 28.7 0.7
CG A:PHE448 5.0 46.9 1.0

Fluorine binding site 3 out of 3 in 2ycn

Go back to Fluorine Binding Sites List in 2ycn
Fluorine binding site 3 out of 3 in the Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Y71F Mutant of Tyrosine Phenol-Lyase From Citrobacter Freundii in Complex with Quinonoid Intermediate Formed with 3-Fluoro-L-Tyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F600

b:43.5
occ:1.00
 F B:P61600 0.0 43.5 1.0
CE1 B:P61600 1.4 32.8 1.0
CZ B:P61600 2.4 31.4 1.0
CD1 B:P61600 2.4 32.4 1.0
OH B:P61600 2.7 36.6 1.0
O B:HOH2414 3.1 44.7 1.0
NH1 B:ARG381 3.2 37.0 1.0
CE2 B:P61600 3.7 29.6 1.0
CG B:P61600 3.7 23.1 1.0
NH2 B:ARG381 3.8 34.5 1.0
CZ B:ARG381 3.8 43.0 1.0
CE B:MET379 3.9 25.9 1.0
SD B:MET379 3.9 29.2 1.0
CD2 B:P61600 4.2 22.4 1.0
CE2 B:PHE448 4.4 60.5 1.0
CE A:MET288 4.5 61.4 1.0
O B:HOH2355 4.5 29.0 1.0
CZ B:PHE36 4.7 33.5 1.0
CE2 A:PHE71 4.8 35.2 1.0
O B:P61600 4.8 29.7 1.0
NE B:ARG381 4.9 33.0 1.0
CE1 B:PHE449 4.9 58.0 1.0
CZ A:PHE71 4.9 37.0 1.0
CB B:P61600 4.9 25.6 1.0
CZ B:PHE449 5.0 61.8 1.0

Reference:

D.Milic, T.V.Demidkina, N.G.Faleev, R.S.Phillips, D.Matkovic-Calogovic, A.A.Antson. Crystallographic Snapshots of Tyrosine Phenol-Lyase Show That Substrate Strain Plays A Role in C-C Bond Cleavage J.Am.Chem.Soc. V. 133 16468 2011.
ISSN: ISSN 0002-7863
PubMed: 21899319
DOI: 10.1021/JA203361G
Page generated: Sun Dec 13 11:42:15 2020

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