Fluorine in PDB 5ci0: Ribonucleotide Reductase Y122 3,5-F2Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 3,5-F2Y Variant:
1.17.4.1;

The structure of Ribonucleotide Reductase Y122 3,5-F2Y Variant, PDB code: 5ci0 was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.81 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.613, 91.613, 205.650, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.2

The structure of Ribonucleotide Reductase Y122 3,5-F2Y Variant also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Fluorine atom in the Ribonucleotide Reductase Y122 3,5-F2Y Variant (pdb code 5ci0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Ribonucleotide Reductase Y122 3,5-F2Y Variant, PDB code: 5ci0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Ribonucleotide Reductase Y122 3,5-F2Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ribonucleotide Reductase Y122 3,5-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:62.6 occ:1.00 F1 A:F2Y122 0.0 62.6 1.0 CE1 A:F2Y122 1.3 57.9 1.0 CZ A:F2Y122 2.4 59.4 1.0 CD1 A:F2Y122 2.4 52.0 1.0 OH A:F2Y122 2.7 59.3 1.0 OD2 A:ASP84 2.9 48.1 1.0 CB A:ASP84 3.2 50.6 1.0 CG A:ASP84 3.3 49.7 1.0 O A:GLN80 3.3 54.1 1.0 CE2 A:F2Y122 3.6 59.2 1.0 CG A:F2Y122 3.6 52.5 1.0 CZ A:PHE208 3.8 53.1 1.0 CB A:HIS118 3.9 45.4 1.0 C A:GLN80 3.9 52.6 1.0 O A:HOH599 4.0 64.3 1.0 CE1 A:PHE208 4.0 52.8 1.0 CD2 A:F2Y122 4.1 55.2 1.0 O A:HIS118 4.2 47.9 1.0 CB A:GLN80 4.2 49.2 1.0 C A:HIS118 4.2 47.5 1.0 O A:HOH587 4.4 76.5 1.0 OD1 A:ASP84 4.4 51.0 1.0 CA A:ASP84 4.4 50.8 1.0 N A:ASP84 4.5 49.6 1.0 N A:SER119 4.6 45.4 1.0 N A:THR81 4.6 53.4 1.0 CA A:GLN80 4.6 50.9 1.0 CA A:HIS118 4.6 48.4 1.0 FE2 A:FEO401 4.7 51.7 1.0 F2 A:F2Y122 4.7 56.8 1.0 CD1 A:ILE234 4.7 40.2 1.0 CA A:THR81 4.7 49.9 1.0 CG A:HIS118 4.8 46.1 1.0 CB A:F2Y122 4.9 47.4 1.0 CA A:SER119 4.9 49.5 1.0 CE2 A:PHE208 5.0 55.9 1.0

Fluorine binding site 2 out of 2 in the Ribonucleotide Reductase Y122 3,5-F2Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ribonucleotide Reductase Y122 3,5-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:56.8 occ:1.00 F2 A:F2Y122 0.0 56.8 1.0 CE2 A:F2Y122 1.3 59.2 1.0 CZ A:F2Y122 2.3 59.4 1.0 CD2 A:F2Y122 2.3 55.2 1.0 OH A:F2Y122 2.7 59.3 1.0 OE1 A:GLN80 3.0 56.2 1.0 CD1 A:ILE231 3.2 47.7 1.0 CD A:GLN80 3.4 52.0 1.0 CE1 A:F2Y122 3.6 57.9 1.0 CG A:F2Y122 3.6 52.5 1.0 NE2 A:GLN80 3.7 52.0 1.0 CD1 A:ILE234 3.8 40.2 1.0 O A:HOH592 3.8 61.6 1.0 CD1 A:F2Y122 4.1 52.0 1.0 CB A:GLN80 4.2 49.2 1.0 CD1 A:ILE125 4.3 44.7 1.0 CD1 A:LEU77 4.3 58.5 1.0 CG A:GLN80 4.4 51.2 1.0 CG1 A:ILE231 4.6 49.8 1.0 OD1 A:ASN227 4.7 49.9 1.0 F1 A:F2Y122 4.7 62.6 1.0 CB A:F2Y122 4.8 47.4 1.0 O A:HOH533 4.9 58.7 1.0 OG A:SER121 4.9 52.7 1.0

P.H.Oyala, K.R.Ravichandran, M.A.Funk, P.A.Stucky, T.A.Stich, C.L.Drennan, R.D.Britt, J.Stubbe. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated Into Enzymes: E. Coli Ribonucleotide Reductase As An Example. J.Am.Chem.Soc. V. 138 7951 2016.
ISSN: ESSN 1520-5126
PubMed: 27276098
DOI: 10.1021/JACS.6B03605