Iron 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:

Fluorine	(F)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Ribonucleotide Reductase Y122 2,3-F2Y Variant (pdb code 5ci1). 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-F2Y Variant, PDB code: 5ci1:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Ribonucleotide Reductase Y122 2,3-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 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:29.8 occ:1.00 FE1 A:FEO401 0.0 29.8 1.0 O A:FEO401 1.9 23.4 1.0 OE1 A:GLU204 2.1 29.4 1.0 OE1 A:GLU238 2.1 32.6 1.0 OE2 A:GLU115 2.2 35.4 1.0 O A:HOH547 2.2 35.1 1.0 ND1 A:HIS241 2.2 31.4 1.0 CD A:GLU238 3.0 35.0 1.0 HG2 A:GLU204 3.0 43.8 1.0 CD A:GLU115 3.1 33.4 1.0 CD A:GLU204 3.1 33.4 1.0 CE1 A:HIS241 3.1 33.7 1.0 HE1 A:HIS241 3.2 40.5 1.0 OE2 A:GLU238 3.3 43.1 1.0 HE1 A:TRP111 3.3 32.0 1.0 FE2 A:FEO401 3.3 29.7 1.0 OE1 A:GLU115 3.3 29.2 1.0 CG A:HIS241 3.3 30.2 1.0 HB2 A:HIS241 3.5 33.7 1.0 CG A:GLU204 3.5 36.5 1.0 HB3 A:HIS241 3.6 33.7 1.0 HA A:GLU238 3.6 34.3 1.0 CB A:HIS241 3.7 28.1 1.0 HE21 A:GLN87 3.7 49.9 1.0 NE1 A:TRP111 4.0 26.7 1.0 OE2 A:GLU204 4.1 36.6 1.0 HG3 A:GLU204 4.2 43.8 1.0 HE1 A:HIS118 4.3 27.7 1.0 NE2 A:HIS241 4.3 27.5 1.0 HB3 A:GLU204 4.3 37.7 1.0 O A:HOH591 4.3 35.5 1.0 OD1 A:ASP84 4.3 36.0 1.0 CG A:GLU238 4.3 31.4 1.0 HD1 A:TRP111 4.4 30.3 1.0 HG3 A:GLN87 4.4 40.3 1.0 CD2 A:HIS241 4.4 29.6 1.0 CG A:GLU115 4.4 21.9 1.0 CA A:GLU238 4.5 28.6 1.0 HB3 A:GLN87 4.5 39.5 1.0 CB A:GLU204 4.5 31.4 1.0 NE2 A:GLN87 4.6 41.6 1.0 HB2 A:GLU238 4.6 35.5 1.0 HG3 A:GLU238 4.6 37.6 1.0 HG2 A:GLU115 4.6 26.3 1.0 CD1 A:TRP111 4.6 25.2 1.0 HG3 A:GLU115 4.6 26.3 1.0 CB A:GLU238 4.7 29.6 1.0 ND1 A:HIS118 4.8 25.1 1.0 OD2 A:ASP84 4.8 29.0 1.0 CE1 A:HIS118 4.8 23.1 1.0 HA A:GLU204 4.9 39.4 1.0

Iron binding site 2 out of 2 in the Ribonucleotide Reductase Y122 2,3-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 2,3-F2Y Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:29.7 occ:1.00 FE2 A:FEO401 0.0 29.7 1.0 OD2 A:ASP84 1.9 29.0 1.0 O A:FEO401 1.9 23.4 1.0 OE1 A:GLU115 2.1 29.2 1.0 ND1 A:HIS118 2.2 25.1 1.0 O A:HOH591 2.4 35.5 1.0 CG A:ASP84 2.7 34.4 1.0 OD1 A:ASP84 2.9 36.0 1.0 O A:HOH547 3.0 35.1 1.0 CE1 A:HIS118 3.0 23.1 1.0 HE1 A:HIS118 3.1 27.7 1.0 CD A:GLU115 3.1 33.4 1.0 FE1 A:FEO401 3.3 29.8 1.0 CG A:HIS118 3.3 23.0 1.0 OE2 A:GLU115 3.5 35.4 1.0 HB2 A:HIS118 3.5 32.4 1.0 HG23 A:ILE234 3.6 30.1 1.0 HB3 A:HIS118 3.7 32.4 1.0 HA A:GLU115 3.7 34.0 1.0 CB A:HIS118 3.8 27.0 1.0 HE1 A:HIS241 3.8 40.5 1.0 OE2 A:GLU238 3.9 43.1 1.0 CB A:ASP84 4.1 24.9 1.0 NE2 A:HIS118 4.2 22.8 1.0 HB3 A:ASP84 4.3 29.9 1.0 CD2 A:HIS118 4.4 26.8 1.0 CG2 A:ILE234 4.4 25.1 1.0 HZ A:PHE208 4.4 39.7 1.0 HG21 A:ILE234 4.4 30.1 1.0 CE1 A:HIS241 4.4 33.7 1.0 CZ A:PHE208 4.4 33.1 1.0 OH A:FY2122 4.4 37.9 0.3 CG A:GLU115 4.4 21.9 1.0 HB3 A:GLU115 4.5 29.3 1.0 HH A:FY2122 4.5 45.4 0.3 CD A:GLU238 4.5 35.0 1.0 ND1 A:HIS241 4.5 31.4 1.0 HB2 A:ASP84 4.5 29.9 1.0 OE1 A:GLU238 4.5 32.6 1.0 CE2 A:PHE208 4.6 35.9 1.0 CA A:GLU115 4.6 28.3 1.0 HE2 A:PHE208 4.6 43.1 1.0 HG22 A:ILE234 4.7 30.1 1.0 F3 A:FY2122 4.7 42.1 0.7 HH A:FY2122 4.7 32.6 0.7 CB A:GLU115 4.7 24.4 1.0 HB2 A:GLN87 4.8 39.5 1.0 HA A:ASP84 4.9 40.9 1.0 CE1 A:PHE208 4.9 32.8 1.0 HG2 A:GLU115 4.9 26.3 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