Iron in PDB 5ci3: Ribonucleotide Reductase Y122 2,3,5-F3Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant:
1.17.4.1;

The structure of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant, PDB code: 5ci3 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)	43.44 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.216, 92.216, 207.044, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 21.2

The structure of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Iron atom in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant (pdb code 5ci3). 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 2,3,5-F3Y Variant, PDB code: 5ci3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Ribonucleotide Reductase Y122 2,3,5-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 2,3,5-F3Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:69.0 occ:1.00 FE1 A:FEO401 0.0 69.0 1.0 O A:FEO401 1.8 52.7 1.0 OE1 A:GLU204 2.0 76.4 1.0 OE1 A:GLU238 2.1 85.0 1.0 O A:HOH546 2.1 49.7 1.0 ND1 A:HIS241 2.2 75.0 1.0 OE2 A:GLU115 2.3 90.2 1.0 CD A:GLU238 2.9 76.3 1.0 CE1 A:HIS241 3.0 72.2 1.0 CD A:GLU204 3.1 80.2 1.0 CD A:GLU115 3.1 83.7 1.0 OE2 A:GLU238 3.1 76.4 1.0 FE2 A:FEO401 3.2 70.4 1.0 OE1 A:GLU115 3.3 84.6 1.0 CG A:HIS241 3.3 74.7 1.0 CG A:GLU204 3.6 79.9 1.0 CB A:HIS241 3.6 64.8 1.0 NE1 A:TRP111 4.0 74.8 1.0 OE2 A:GLU204 4.1 74.5 1.0 O A:HOH561 4.1 89.8 1.0 NE2 A:HIS241 4.2 71.9 1.0 CG A:GLU238 4.3 75.2 1.0 CD2 A:HIS241 4.3 73.9 1.0 OD1 A:ASP84 4.4 75.7 1.0 CA A:GLU238 4.4 70.0 1.0 CG A:GLU115 4.5 84.0 1.0 CB A:GLU204 4.5 78.0 1.0 CD1 A:TRP111 4.6 75.7 1.0 NE2 A:GLN87 4.6 76.1 1.0 CB A:GLU238 4.7 71.9 1.0 CE1 A:HIS118 4.7 63.3 1.0 ND1 A:HIS118 4.8 61.0 1.0 OD2 A:ASP84 4.9 64.9 1.0 CG A:GLN87 4.9 75.8 1.0

Iron binding site 2 out of 2 in the Ribonucleotide Reductase Y122 2,3,5-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 2,3,5-F3Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:70.4 occ:1.00 FE2 A:FEO401 0.0 70.4 1.0 O A:FEO401 1.8 52.7 1.0 OD2 A:ASP84 2.0 64.9 1.0 OE1 A:GLU115 2.1 84.6 1.0 ND1 A:HIS118 2.2 61.0 1.0 O A:HOH561 2.3 89.8 1.0 CG A:ASP84 2.8 72.0 1.0 O A:HOH546 2.9 49.7 1.0 OD1 A:ASP84 2.9 75.7 1.0 CE1 A:HIS118 2.9 63.3 1.0 CD A:GLU115 3.1 83.7 1.0 FE1 A:FEO401 3.2 69.0 1.0 CG A:HIS118 3.3 62.8 1.0 OE2 A:GLU115 3.6 90.2 1.0 OE2 A:GLU238 3.8 76.4 1.0 CB A:HIS118 3.8 60.7 1.0 NE2 A:HIS118 4.1 63.0 1.0 CB A:ASP84 4.2 70.3 1.0 CD2 A:HIS118 4.3 58.2 1.0 CE1 A:HIS241 4.4 72.2 1.0 CZ A:PHE208 4.4 81.2 1.0 CD A:GLU238 4.4 76.3 1.0 CG2 A:ILE234 4.4 62.3 1.0 ND1 A:HIS241 4.4 75.0 1.0 CE2 A:PHE208 4.5 82.0 1.0 CG A:GLU115 4.5 84.0 1.0 OE1 A:GLU238 4.5 85.0 1.0 CA A:GLU115 4.6 73.0 1.0 CB A:GLU115 4.7 75.3 1.0 CE1 A:PHE208 5.0 80.1 1.0 OE1 A:GLU204 5.0 76.4 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