Fluorine in PDB 5ci1: Ribonucleotide Reductase Y122 2,3-F2Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 2,3-F2Y Variant:
1.17.4.1;

The structure of Ribonucleotide Reductase Y122 2,3-F2Y Variant, PDB code: 5ci1 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)	38.00 / 1.95
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.589, 90.589, 209.468, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 18.3

The structure of Ribonucleotide Reductase Y122 2,3-F2Y Variant also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Ribonucleotide Reductase Y122 2,3-F2Y Variant (pdb code 5ci1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Ribonucleotide Reductase Y122 2,3-F2Y Variant, PDB code: 5ci1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Ribonucleotide Reductase Y122 2,3-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 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:31.2 occ:0.67 F2 A:FY2122 0.0 31.2 0.7 CD2 A:FY2122 0.7 31.4 0.3 CE2 A:FY2122 1.0 30.2 0.3 HD2 A:FY2122 1.0 37.7 0.3 CD1 A:FY2122 1.3 26.2 0.7 HE2 A:FY2122 1.4 36.3 0.3 CG A:FY2122 2.0 27.4 0.3 CZ A:FY2122 2.3 31.1 0.3 CE1 A:FY2122 2.3 28.6 0.7 HA A:SER119 2.3 31.6 0.4 HA A:SER119 2.3 31.9 0.6 CG A:FY2122 2.4 25.9 0.7 HB1 A:FY2122 2.4 31.4 0.7 HA A:THR81 2.6 32.6 1.0 F3 A:FY2122 2.7 42.1 0.7 CB A:FY2122 2.9 26.2 0.7 CD1 A:FY2122 2.9 33.1 0.3 CE1 A:FY2122 3.0 34.6 0.3 HB1 A:FY2122 3.0 32.0 0.3 CB A:FY2122 3.1 26.7 0.3 O A:HIS118 3.2 26.8 1.0 CA A:SER119 3.3 26.3 0.4 CA A:SER119 3.3 26.6 0.6 HB2 A:ASP84 3.3 29.9 1.0 HB2 A:FY2122 3.4 31.4 0.7 OH A:FY2122 3.4 37.9 0.3 HG23 A:THR81 3.5 38.4 1.0 CA A:THR81 3.5 27.2 1.0 CZ A:FY2122 3.6 29.6 0.7 H A:FY2122 3.6 30.4 0.3 CD2 A:FY2122 3.6 35.4 0.7 H A:FY2122 3.6 30.4 0.7 C A:HIS118 3.6 27.4 1.0 N A:SER119 3.7 27.3 0.6 HB2 A:FY2122 3.7 32.0 0.3 N A:SER119 3.7 27.1 0.4 HB3 A:SER119 3.9 32.4 0.4 OG1 A:THR81 3.9 31.0 1.0 O A:GLN80 3.9 28.3 1.0 HB3 A:ASP84 4.0 29.9 1.0 O A:SER119 4.0 22.6 0.6 C A:SER119 4.1 28.2 0.6 CE2 A:FY2122 4.1 30.2 0.7 N A:THR81 4.1 26.6 1.0 CB A:SER119 4.1 27.0 0.4 HH A:FY2122 4.1 45.4 0.3 CB A:THR81 4.1 28.8 1.0 CB A:ASP84 4.1 24.9 1.0 C A:SER119 4.1 27.3 0.4 CA A:FY2122 4.2 25.9 0.7 F2 A:FY2122 4.2 37.0 0.3 OG A:SER119 4.2 26.1 0.6 HG1 A:THR81 4.2 37.2 1.0 O A:SER119 4.2 28.4 0.4 CA A:FY2122 4.2 27.3 0.3 HB3 A:HIS118 4.2 32.4 1.0 CB A:SER119 4.2 24.6 0.6 CG2 A:THR81 4.2 32.0 1.0 C A:GLN80 4.2 30.3 1.0 N A:FY2122 4.3 25.3 0.7 N A:FY2122 4.3 25.3 0.3 HB2 A:SER119 4.3 32.4 0.4 H A:SER119 4.3 32.7 0.6 F3 A:FY2122 4.3 38.3 0.3 H A:SER119 4.4 32.6 0.4 HB3 A:SER119 4.4 29.5 0.6 HD2 A:FY2122 4.4 42.5 0.7 O A:THR81 4.5 31.7 1.0 C A:THR81 4.5 31.6 1.0 HB3 A:GLN80 4.6 34.5 1.0 HG A:SER121 4.6 37.5 0.5 H A:ASP84 4.6 37.0 1.0 H A:THR81 4.6 31.9 1.0 HA A:FY2122 4.7 31.1 0.7 HA A:FY2122 4.7 32.7 0.3 HH A:FY2122 4.7 32.6 0.7 OH A:FY2122 4.7 27.1 0.7 HG22 A:THR81 4.7 38.4 1.0 HB2 A:HIS118 4.8 32.4 1.0 CB A:HIS118 4.8 27.0 1.0 CA A:HIS118 4.8 29.6 1.0 O A:HOH525 4.8 32.1 1.0 HG A:SER119 4.9 31.3 0.6 HG21 A:THR81 4.9 38.4 1.0

Fluorine binding site 2 out of 4 in the Ribonucleotide Reductase Y122 2,3-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 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:37.0 occ:0.33 F2 A:FY2122 0.0 37.0 0.3 HD2 A:FY2122 0.3 42.5 0.7 CD2 A:FY2122 0.7 35.4 0.7 CD1 A:FY2122 1.3 33.1 0.3 CE2 A:FY2122 1.8 30.2 0.7 CG A:FY2122 1.8 25.9 0.7 HE2 A:FY2122 2.2 36.2 0.7 HA A:FY2122 2.3 31.1 0.7 HA A:FY2122 2.3 32.7 0.3 CG A:FY2122 2.3 27.4 0.3 CE1 A:FY2122 2.4 34.6 0.3 CB A:FY2122 2.6 26.2 0.7 HD11 A:LEU77 2.7 47.8 1.0 F3 A:FY2122 2.7 38.3 0.3 HB2 A:FY2122 2.8 32.0 0.3 HB2 A:FY2122 2.8 31.4 0.7 CB A:FY2122 2.8 26.7 0.3 HD12 A:ILE125 2.8 37.5 1.0 HD12 A:LEU77 2.8 47.8 1.0 CA A:FY2122 2.9 25.9 0.7 CA A:FY2122 2.9 27.3 0.3 CD1 A:FY2122 3.0 26.2 0.7 CZ A:FY2122 3.0 29.6 0.7 CD1 A:LEU77 3.1 39.8 1.0 HD13 A:LEU77 3.4 47.8 1.0 HB1 A:FY2122 3.5 31.4 0.7 CE1 A:FY2122 3.5 28.6 0.7 N A:FY2122 3.6 25.3 0.3 N A:FY2122 3.6 25.3 0.7 CD2 A:FY2122 3.6 31.4 0.3 CD1 A:ILE125 3.6 31.2 1.0 CZ A:FY2122 3.6 31.1 0.3 HD13 A:ILE125 3.6 37.5 1.0 HB1 A:FY2122 3.7 32.0 0.3 H A:FY2122 3.8 30.4 0.3 H A:FY2122 3.9 30.4 0.7 HD11 A:ILE125 4.1 37.5 1.0 HB A:ILE125 4.1 33.6 1.0 CE2 A:FY2122 4.1 30.2 0.3 F2 A:FY2122 4.2 31.2 0.7 C A:FY2122 4.2 28.3 0.7 C A:FY2122 4.2 29.1 0.3 OH A:FY2122 4.2 27.1 0.7 HD11 A:ILE231 4.3 40.4 1.0 C A:SER121 4.3 30.3 1.0 HG1 A:THR81 4.3 37.2 1.0 HD2 A:FY2122 4.4 37.7 0.3 HG A:SER121 4.4 37.5 0.5 HB2 A:GLN80 4.4 34.5 1.0 OG A:SER121 4.4 31.2 1.0 O A:SER121 4.4 25.3 1.0 CG A:LEU77 4.5 37.1 1.0 O A:FY2122 4.5 29.5 0.7 O A:FY2122 4.5 30.4 0.3 OG1 A:THR81 4.5 31.0 1.0 HG A:LEU77 4.6 44.5 1.0 HB3 A:GLN80 4.6 34.5 1.0 HD11 A:ILE234 4.6 33.7 1.0 HD12 A:ILE234 4.7 33.7 1.0 HE22 A:GLN80 4.7 40.5 1.0 O A:HIS118 4.7 26.8 1.0 CG1 A:ILE125 4.7 31.4 1.0 HH A:FY2122 4.7 45.4 0.3 OH A:FY2122 4.8 37.9 0.3 F3 A:FY2122 4.8 42.1 0.7 HD13 A:ILE231 4.8 40.4 1.0 O A:HOH569 4.8 33.2 1.0 CB A:ILE125 4.8 28.0 1.0 HA A:LEU77 4.8 32.3 1.0 HD13 A:ILE234 4.8 33.7 1.0 NE2 A:GLN80 4.8 33.7 1.0 HH A:FY2122 4.9 32.6 0.7 HG21 A:ILE230 4.9 30.3 1.0 HG21 A:ILE125 4.9 34.2 1.0 CD1 A:ILE231 4.9 33.7 1.0 CD1 A:ILE234 4.9 28.1 1.0 CB A:GLN80 5.0 28.7 1.0 O A:LEU77 5.0 29.6 1.0 HG13 A:ILE125 5.0 37.7 1.0

Fluorine binding site 3 out of 4 in the Ribonucleotide Reductase Y122 2,3-F2Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ribonucleotide Reductase Y122 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:42.1 occ:0.67 F3 A:FY2122 0.0 42.1 0.7 OH A:FY2122 0.9 37.9 0.3 CZ A:FY2122 1.2 31.1 0.3 CE1 A:FY2122 1.3 28.6 0.7 CE2 A:FY2122 1.7 30.2 0.3 HE2 A:FY2122 1.7 36.3 0.3 HH A:FY2122 1.8 45.4 0.3 CZ A:FY2122 2.4 29.6 0.7 CD1 A:FY2122 2.4 26.2 0.7 HH A:FY2122 2.4 32.6 0.7 HB2 A:ASP84 2.4 29.9 1.0 CE1 A:FY2122 2.5 34.6 0.3 F2 A:FY2122 2.7 31.2 0.7 OH A:FY2122 2.7 27.1 0.7 CD2 A:FY2122 3.0 31.4 0.3 HB3 A:HIS118 3.0 32.4 1.0 OD2 A:ASP84 3.1 29.0 1.0 O A:GLN80 3.1 28.3 1.0 HB3 A:GLN80 3.2 34.5 1.0 CB A:ASP84 3.2 24.9 1.0 HZ A:PHE208 3.2 39.7 1.0 F3 A:FY2122 3.3 38.3 0.3 CG A:ASP84 3.4 34.4 1.0 HE1 A:PHE208 3.4 39.4 1.0 HB3 A:ASP84 3.5 29.9 1.0 CD1 A:FY2122 3.6 33.1 0.3 CE2 A:FY2122 3.6 30.2 0.7 CG A:FY2122 3.6 25.9 0.7 HD2 A:FY2122 3.7 37.7 0.3 HD13 A:ILE234 3.7 33.7 1.0 C A:GLN80 3.7 30.3 1.0 CG A:FY2122 3.8 27.4 0.3 CZ A:PHE208 3.9 33.1 1.0 HA A:THR81 3.9 32.6 1.0 CB A:HIS118 3.9 27.0 1.0 CE1 A:PHE208 3.9 32.8 1.0 HB2 A:HIS118 4.0 32.4 1.0 H A:ASP84 4.0 37.0 1.0 CB A:GLN80 4.1 28.7 1.0 CD2 A:FY2122 4.1 35.4 0.7 O A:HIS118 4.2 26.8 1.0 C A:HIS118 4.3 27.4 1.0 O A:HOH591 4.3 35.5 1.0 HA A:SER119 4.4 31.6 0.4 HA A:SER119 4.4 31.9 0.6 HE2 A:FY2122 4.4 36.2 0.7 CA A:GLN80 4.4 28.7 1.0 N A:THR81 4.4 26.6 1.0 OD1 A:ASP84 4.4 36.0 1.0 HB2 A:GLN80 4.4 34.5 1.0 CA A:ASP84 4.5 34.1 1.0 HA A:GLN80 4.5 34.5 1.0 HG21 A:ILE234 4.5 30.1 1.0 N A:ASP84 4.5 30.9 1.0 CA A:THR81 4.6 27.2 1.0 CD1 A:ILE234 4.6 28.1 1.0 FE2 A:FEO401 4.7 29.7 1.0 CA A:HIS118 4.7 29.6 1.0 HD11 A:ILE234 4.7 33.7 1.0 N A:SER119 4.7 27.3 0.6 N A:SER119 4.8 27.1 0.4 F2 A:FY2122 4.8 37.0 0.3 HB1 A:FY2122 4.8 31.4 0.7 CG A:HIS118 4.9 23.0 1.0 CB A:FY2122 4.9 26.2 0.7 HA A:HIS118 5.0 35.6 1.0

Fluorine binding site 4 out of 4 in the Ribonucleotide Reductase Y122 2,3-F2Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ribonucleotide Reductase Y122 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:F122 b:38.3 occ:0.33 F3 A:FY2122 0.0 38.3 0.3 CE2 A:FY2122 0.9 30.2 0.7 CZ A:FY2122 0.9 29.6 0.7 HE2 A:FY2122 1.2 36.2 0.7 CE1 A:FY2122 1.3 34.6 0.3 OH A:FY2122 1.6 27.1 0.7 CE1 A:FY2122 2.2 28.6 0.7 CD2 A:FY2122 2.2 35.4 0.7 HH A:FY2122 2.3 32.6 0.7 CD1 A:FY2122 2.3 33.1 0.3 CZ A:FY2122 2.4 31.1 0.3 HH A:FY2122 2.4 45.4 0.3 F2 A:FY2122 2.7 37.0 0.3 OH A:FY2122 2.8 37.9 0.3 HD13 A:ILE234 2.8 33.7 1.0 HD2 A:FY2122 2.9 42.5 0.7 HD12 A:ILE234 3.0 33.7 1.0 CD1 A:FY2122 3.0 26.2 0.7 HB3 A:GLN80 3.0 34.5 1.0 CG A:FY2122 3.1 25.9 0.7 OE1 A:GLN80 3.1 44.2 1.0 CD1 A:ILE234 3.2 28.1 1.0 F3 A:FY2122 3.3 42.1 0.7 HD12 A:ILE231 3.4 40.4 1.0 HD11 A:ILE234 3.4 33.7 1.0 HD11 A:ILE231 3.5 40.4 1.0 CD A:GLN80 3.6 30.3 1.0 CG A:FY2122 3.6 27.4 0.3 CE2 A:FY2122 3.6 30.2 0.3 HD13 A:ILE231 3.6 40.4 1.0 CD1 A:ILE231 3.7 33.7 1.0 HB2 A:GLN80 3.8 34.5 1.0 CB A:GLN80 3.8 28.7 1.0 HG21 A:ILE234 4.0 30.1 1.0 NE2 A:GLN80 4.1 33.7 1.0 CD2 A:FY2122 4.1 31.4 0.3 HE1 A:PHE208 4.1 39.4 1.0 HE22 A:GLN80 4.1 40.5 1.0 CG A:GLN80 4.2 28.4 1.0 F2 A:FY2122 4.3 31.2 0.7 HD12 A:LEU77 4.3 47.8 1.0 HE2 A:FY2122 4.4 36.3 0.3 HG2 A:GLN80 4.5 34.1 1.0 CB A:FY2122 4.5 26.2 0.7 HG A:SER121 4.6 37.5 0.5 HB3 A:HIS118 4.6 32.4 1.0 HE21 A:GLN80 4.6 40.5 1.0 CG1 A:ILE234 4.7 24.3 1.0 OG A:SER121 4.7 31.2 1.0 HD12 A:ILE125 4.7 37.5 1.0 HA A:FY2122 4.8 31.1 0.7 CB A:FY2122 4.8 26.7 0.3 HA A:FY2122 4.8 32.7 0.3 HG22 A:ILE230 4.8 30.3 1.0 HB2 A:FY2122 4.9 31.4 0.7 O A:HIS118 4.9 26.8 1.0 CG2 A:ILE234 4.9 25.1 1.0 HD11 A:LEU77 5.0 47.8 1.0 CD1 A:LEU77 5.0 39.8 1.0 HB2 A:FY2122 5.0 32.0 0.3 CE1 A:PHE208 5.0 32.8 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