Iron in PDB 2xof: Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli

All present enzymatic activity of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli:
1.17.4.1;

The structure of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli, PDB code: 2xof was solved by K.Yokoyama, U.Uhlin, J.Stubbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.68 / 2.20
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	137.103, 137.103, 108.973, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.4

The binding sites of Iron atom in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli (pdb code 2xof). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli, PDB code: 2xof:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:23.1 occ:1.00 FE1 A:FEO400 0.0 23.1 1.0 O A:FEO400 2.0 20.6 1.0 OD2 A:ASP84 2.0 22.0 1.0 ND1 A:HIS118 2.1 18.3 1.0 OE1 A:GLU115 2.2 18.7 1.0 O A:HOH2136 2.4 23.5 1.0 CG A:ASP84 2.8 21.5 1.0 CE1 A:HIS118 2.9 18.4 1.0 OD1 A:ASP84 3.0 21.6 1.0 O A:HOH2190 3.1 22.4 1.0 CD A:GLU115 3.2 19.8 1.0 CG A:HIS118 3.2 18.9 1.0 FE2 A:FEO400 3.2 20.3 1.0 OE2 A:GLU115 3.6 20.1 1.0 CB A:HIS118 3.7 19.3 1.0 OE1 A:GLU238 3.9 20.1 1.0 NE2 A:HIS118 4.1 17.8 1.0 CB A:ASP84 4.2 21.5 1.0 CD2 A:HIS118 4.3 17.8 1.0 CG2 A:ILE234 4.3 19.4 1.0 CE1 A:HIS241 4.4 17.5 1.0 OE2 A:GLU238 4.5 19.4 1.0 CD A:GLU238 4.5 19.7 1.0 ND1 A:HIS241 4.5 17.9 1.0 CE2 A:PHE208 4.5 20.2 1.0 CZ A:PHE208 4.5 19.8 1.0 CG A:GLU115 4.6 19.8 1.0 CA A:GLU115 4.7 20.0 1.0 CB A:GLU115 4.8 19.7 1.0 OH A:NIY122 4.9 28.4 1.0

Iron binding site 2 out of 4 in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:20.3 occ:1.00 FE2 A:FEO400 0.0 20.3 1.0 O A:FEO400 1.8 20.6 1.0 O A:HOH2190 2.0 22.4 1.0 OE2 A:GLU115 2.0 20.1 1.0 OE2 A:GLU204 2.1 20.7 1.0 ND1 A:HIS241 2.3 17.9 1.0 OE2 A:GLU238 2.3 19.4 1.0 CD A:GLU115 2.9 19.8 1.0 CE1 A:HIS241 3.1 17.5 1.0 CD A:GLU204 3.1 19.5 1.0 CD A:GLU238 3.2 19.7 1.0 OE1 A:GLU115 3.2 18.7 1.0 FE1 A:FEO400 3.2 23.1 1.0 CG A:HIS241 3.3 18.0 1.0 OE1 A:GLU238 3.4 20.1 1.0 CB A:HIS241 3.7 18.2 1.0 CG A:GLU204 3.7 18.7 1.0 NE1 A:TRP111 4.0 18.4 1.0 OE1 A:GLU204 4.1 19.8 1.0 NE2 A:HIS241 4.3 17.5 1.0 OD1 A:ASP84 4.3 21.6 1.0 CG A:GLU115 4.3 19.8 1.0 O A:HOH2136 4.3 23.5 1.0 CD2 A:HIS241 4.4 17.1 1.0 CG A:GLU238 4.5 18.8 1.0 NE2 A:GLN87 4.5 20.6 1.0 CD1 A:TRP111 4.5 17.9 1.0 CA A:GLU238 4.6 18.8 1.0 CB A:GLU204 4.6 18.9 1.0 ND1 A:HIS118 4.8 18.3 1.0 CE1 A:HIS118 4.8 18.4 1.0 OD2 A:ASP84 4.8 22.0 1.0 CB A:GLU238 4.8 19.0 1.0 CG A:GLN87 4.9 20.6 1.0 CG A:ASP84 5.0 21.5 1.0

Iron binding site 3 out of 4 in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:24.7 occ:1.00 FE1 B:FEO400 0.0 24.7 1.0 OD2 B:ASP84 2.0 24.4 1.0 ND1 B:HIS118 2.1 19.2 1.0 OE1 B:GLU115 2.1 20.6 1.0 O B:FEO400 2.1 20.4 1.0 O B:HOH2063 2.2 24.2 1.0 CE1 B:HIS118 2.9 19.5 1.0 CG B:ASP84 2.9 22.8 1.0 OD1 B:ASP84 3.1 22.9 1.0 CD B:GLU115 3.2 19.7 1.0 O B:HOH2117 3.2 19.6 1.0 FE2 B:FEO400 3.2 22.4 1.0 CG B:HIS118 3.3 19.5 1.0 OE2 B:GLU115 3.6 18.6 1.0 CB B:HIS118 3.8 19.5 1.0 OE2 B:GLU238 4.0 23.8 1.0 NE2 B:HIS118 4.1 18.8 1.0 CB B:ASP84 4.2 22.2 1.0 CD2 B:HIS118 4.3 19.5 1.0 CG2 B:ILE234 4.4 19.8 1.0 CE1 B:HIS241 4.5 22.2 1.0 CZ B:PHE208 4.5 23.4 1.0 CG B:GLU115 4.5 19.1 1.0 CD B:GLU238 4.5 23.4 1.0 ND1 B:HIS241 4.5 21.9 1.0 CE2 B:PHE208 4.5 23.4 1.0 OE1 B:GLU238 4.6 23.7 1.0 CA B:GLU115 4.6 19.4 1.0 CB B:GLU115 4.7 19.3 1.0 CE1 B:PHE208 5.0 23.4 1.0

Iron binding site 4 out of 4 in the Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleotide Reductase Y122NO2Y Modified R2 Subunit of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:22.4 occ:1.00 FE2 B:FEO400 0.0 22.4 1.0 O B:FEO400 1.8 20.4 1.0 O B:HOH2117 2.1 19.6 1.0 OE2 B:GLU115 2.2 18.6 1.0 OE2 B:GLU204 2.2 21.7 1.0 OE1 B:GLU238 2.3 23.7 1.0 ND1 B:HIS241 2.3 21.9 1.0 CD B:GLU115 3.0 19.7 1.0 CD B:GLU238 3.1 23.4 1.0 CD B:GLU204 3.2 22.0 1.0 OE1 B:GLU115 3.2 20.6 1.0 CE1 B:HIS241 3.2 22.2 1.0 FE1 B:FEO400 3.2 24.7 1.0 OE2 B:GLU238 3.2 23.8 1.0 CG B:HIS241 3.4 23.0 1.0 CB B:HIS241 3.7 22.9 1.0 CG B:GLU204 3.8 21.9 1.0 NE1 B:TRP111 4.0 22.1 1.0 OE1 B:GLU204 4.2 21.8 1.0 O B:HOH2063 4.3 24.2 1.0 NE2 B:HIS241 4.4 21.6 1.0 OD1 B:ASP84 4.4 22.9 1.0 CG B:GLU115 4.4 19.1 1.0 CG B:GLU238 4.4 21.7 1.0 CD2 B:HIS241 4.5 21.5 1.0 NE2 B:GLN87 4.5 20.4 1.0 CB B:GLU204 4.5 21.9 1.0 CA B:GLU238 4.5 21.5 1.0 CD1 B:TRP111 4.6 21.7 1.0 CE1 B:HIS118 4.7 19.5 1.0 ND1 B:HIS118 4.7 19.2 1.0 OD2 B:ASP84 4.8 24.4 1.0 CB B:GLU238 4.8 21.4 1.0 CG B:GLN87 5.0 21.8 1.0 CG B:ASP84 5.0 22.8 1.0

K.Yokoyama, U.Uhlin, J.Stubbe. A Hot Oxidant, 3-No(2)Y(122) Radical, Unmasks Conformational Gating in Ribonucleotide Reductase. J.Am.Chem.Soc. V. 132 15368 2010.
ISSN: ISSN 0002-7863
PubMed: 20929229
DOI: 10.1021/JA1069344