Iron 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:

Fluorine

(F)

2 atoms

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

Iron 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 Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase Y122 3,5-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.2 occ:1.00 FE1 A:FEO401 0.0 48.2 1.0 O A:FEO401 1.8 48.4 1.0 OE1 A:GLU204 2.0 53.2 1.0 OE1 A:GLU238 2.0 53.4 1.0 OE2 A:GLU115 2.1 60.8 1.0 ND1 A:HIS241 2.2 51.2 1.0 O A:HOH545 2.2 37.8 1.0 CD A:GLU238 3.0 54.3 1.0 CE1 A:HIS241 3.0 53.5 1.0 CD A:GLU115 3.0 56.2 1.0 CD A:GLU204 3.0 54.7 1.0 FE2 A:FEO401 3.2 51.7 1.0 OE2 A:GLU238 3.3 58.0 1.0 OE1 A:GLU115 3.3 55.4 1.0 CG A:HIS241 3.3 53.7 1.0 CG A:GLU204 3.6 54.7 1.0 CB A:HIS241 3.7 52.5 1.0 OE2 A:GLU204 4.0 50.5 1.0 NE1 A:TRP111 4.1 54.4 1.0 O A:HOH587 4.2 76.5 1.0 NE2 A:HIS241 4.2 51.5 1.0 CG A:GLU238 4.3 56.6 1.0 OD1 A:ASP84 4.3 51.0 1.0 CD2 A:HIS241 4.3 53.2 1.0 CG A:GLU115 4.4 55.0 1.0 CA A:GLU238 4.5 48.6 1.0 CB A:GLU204 4.5 53.4 1.0 NE2 A:GLN87 4.6 58.0 1.0 CE1 A:HIS118 4.7 47.2 1.0 ND1 A:HIS118 4.7 47.8 1.0 CB A:GLU238 4.7 53.3 1.0 CD1 A:TRP111 4.8 50.3 1.0 OD2 A:ASP84 4.8 48.1 1.0 CG A:ASP84 5.0 49.7 1.0

Iron 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 Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase Y122 3,5-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:51.7 occ:1.00 FE2 A:FEO401 0.0 51.7 1.0 O A:FEO401 1.8 48.4 1.0 OD2 A:ASP84 2.0 48.1 1.0 OE1 A:GLU115 2.0 55.4 1.0 ND1 A:HIS118 2.1 47.8 1.0 O A:HOH587 2.3 76.5 1.0 CG A:ASP84 2.8 49.7 1.0 CE1 A:HIS118 2.9 47.2 1.0 OD1 A:ASP84 3.0 51.0 1.0 O A:HOH545 3.0 37.8 1.0 CD A:GLU115 3.1 56.2 1.0 FE1 A:FEO401 3.2 48.2 1.0 CG A:HIS118 3.3 46.1 1.0 OE2 A:GLU115 3.4 60.8 1.0 CB A:HIS118 3.7 45.4 1.0 OE2 A:GLU238 4.0 58.0 1.0 NE2 A:HIS118 4.1 46.6 1.0 CB A:ASP84 4.2 50.6 1.0 CZ A:PHE208 4.3 53.1 1.0 CD2 A:HIS118 4.3 47.0 1.0 CE1 A:HIS241 4.3 53.5 1.0 OE1 A:GLU238 4.4 53.4 1.0 CG A:GLU115 4.4 55.0 1.0 CE2 A:PHE208 4.4 55.9 1.0 ND1 A:HIS241 4.5 51.2 1.0 CD A:GLU238 4.5 54.3 1.0 CG2 A:ILE234 4.5 40.6 1.0 CA A:GLU115 4.6 48.1 1.0 F1 A:F2Y122 4.7 62.6 1.0 CB A:GLU115 4.7 49.6 1.0 CE1 A:PHE208 4.9 52.8 1.0 OE1 A:GLU204 5.0 53.2 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