Iron in PDB 5ci2: Ribonucleotide Reductase Y122 2,3,6-F3Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 2,3,6-F3Y Variant:
1.17.4.1;

The structure of Ribonucleotide Reductase Y122 2,3,6-F3Y Variant, PDB code: 5ci2 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)	44.63 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.420, 91.420, 206.607, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19.7

The structure of Ribonucleotide Reductase Y122 2,3,6-F3Y Variant also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Iron atom in the Ribonucleotide Reductase Y122 2,3,6-F3Y Variant (pdb code 5ci2). 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 2,3,6-F3Y Variant, PDB code: 5ci2:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Ribonucleotide Reductase Y122 2,3,6-F3Y 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 2,3,6-F3Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:58.1 occ:1.00 FE1 A:FEO401 0.0 58.1 1.0 O A:FEO401 1.8 63.7 1.0 OE1 A:GLU204 2.0 64.8 1.0 OE1 A:GLU238 2.0 71.1 1.0 ND1 A:HIS241 2.2 59.6 1.0 O A:HOH553 2.2 54.1 1.0 OE2 A:GLU115 2.2 64.9 1.0 CD A:GLU238 2.9 70.2 1.0 CE1 A:HIS241 3.0 60.2 1.0 CD A:GLU115 3.0 60.0 1.0 CD A:GLU204 3.0 65.3 1.0 OE1 A:GLU115 3.1 57.7 1.0 OE2 A:GLU238 3.1 71.7 1.0 FE2 A:FEO401 3.2 58.8 1.0 CG A:HIS241 3.3 60.7 1.0 CG A:GLU204 3.7 66.1 1.0 CB A:HIS241 3.7 59.0 1.0 OE2 A:GLU204 4.0 65.1 1.0 NE1 A:TRP111 4.0 61.8 1.0 NE2 A:HIS241 4.2 58.9 1.0 OD1 A:ASP84 4.2 63.5 1.0 O A:HOH566 4.2 79.4 1.0 CG A:GLU238 4.2 68.7 1.0 CD2 A:HIS241 4.3 59.4 1.0 CG A:GLU115 4.4 58.8 1.0 CA A:GLU238 4.4 60.5 1.0 CB A:GLU204 4.5 64.5 1.0 CD1 A:TRP111 4.7 59.8 1.0 CB A:GLU238 4.7 65.0 1.0 CE1 A:HIS118 4.7 57.4 1.0 ND1 A:HIS118 4.7 55.1 1.0 NE2 A:GLN87 4.8 61.8 1.0 OD2 A:ASP84 4.9 54.2 1.0

Iron binding site 2 out of 2 in the Ribonucleotide Reductase Y122 2,3,6-F3Y 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 2,3,6-F3Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:58.8 occ:1.00 FE2 A:FEO401 0.0 58.8 1.0 O A:FEO401 1.8 63.7 1.0 OD2 A:ASP84 2.0 54.2 1.0 OE1 A:GLU115 2.0 57.7 1.0 ND1 A:HIS118 2.1 55.1 1.0 O A:HOH566 2.3 79.4 1.0 CG A:ASP84 2.6 59.6 1.0 OD1 A:ASP84 2.7 63.5 1.0 CE1 A:HIS118 2.9 57.4 1.0 O A:HOH553 3.0 54.1 1.0 CD A:GLU115 3.2 60.0 1.0 FE1 A:FEO401 3.2 58.1 1.0 CG A:HIS118 3.3 52.0 1.0 OE2 A:GLU115 3.7 64.9 1.0 CB A:HIS118 3.7 48.5 1.0 OE2 A:GLU238 3.8 71.7 1.0 CB A:ASP84 4.1 60.2 1.0 NE2 A:HIS118 4.1 56.3 1.0 CZ A:PHE208 4.3 69.6 1.0 CD2 A:HIS118 4.3 53.0 1.0 CE1 A:HIS241 4.3 60.2 1.0 CD A:GLU238 4.4 70.2 1.0 CE2 A:PHE208 4.4 70.5 1.0 CG A:GLU115 4.4 58.8 1.0 OE1 A:GLU238 4.4 71.1 1.0 CA A:GLU115 4.5 55.2 1.0 CG2 A:ILE234 4.5 52.2 1.0 ND1 A:HIS241 4.5 59.6 1.0 CB A:GLU115 4.6 56.8 1.0 F3 A:51T122 4.8 65.9 0.6 CE1 A:PHE208 4.9 69.1 1.0 OE1 A:GLU204 5.0 64.8 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