Iron in PDB 1piy: Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH

All present enzymatic activity of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH:
1.17.4.1;

The structure of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH, PDB code: 1piy was solved by W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger Jr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.08 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.900, 84.600, 114.100, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 24.6

The structure of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH also contains other interesting chemical elements:

Mercury

(Hg)

14 atoms

The binding sites of Iron atom in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH (pdb code 1piy). 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 R2 Soaked with Ferrous Ion at Neutral pH, PDB code: 1piy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe376 b:24.1 occ:1.00 OD1 A:ASP84 1.9 13.9 1.0 ND1 A:HIS118 2.1 11.5 1.0 OE1 A:GLU115 2.1 13.8 1.0 OE2 A:GLU238 2.2 13.5 1.0 CE1 A:HIS118 2.8 11.4 1.0 CG A:ASP84 2.8 13.5 1.0 OD2 A:ASP84 3.0 13.8 1.0 CD A:GLU115 3.0 13.5 1.0 CD A:GLU238 3.3 13.4 1.0 CG A:HIS118 3.3 11.6 1.0 CZ A:PHE208 3.5 16.4 1.0 OE2 A:GLU115 3.5 13.9 1.0 FE A:FE377 3.6 25.2 1.0 CB A:HIS118 3.8 11.8 1.0 CE2 A:PHE208 4.0 16.4 1.0 NE2 A:HIS118 4.0 11.5 1.0 CE1 A:PHE208 4.1 16.4 1.0 OE1 A:GLU238 4.1 13.6 1.0 CG A:GLU238 4.2 13.2 1.0 CB A:ASP84 4.2 13.3 1.0 CG A:GLU115 4.2 13.1 1.0 CD2 A:HIS118 4.3 11.5 1.0 CG2 A:ILE234 4.3 12.8 1.0 CA A:GLU115 4.3 12.4 1.0 CB A:GLU115 4.3 12.6 1.0 CE1 A:HIS241 4.8 12.0 1.0 CA A:ASP84 4.8 13.1 1.0 ND1 A:HIS241 4.8 12.0 1.0 CD2 A:PHE208 4.9 16.3 1.0 OH A:TYR122 5.0 14.1 1.0

Iron binding site 2 out of 4 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe377 b:25.2 occ:1.00 OE1 A:GLU238 1.7 13.6 1.0 OE2 A:GLU115 2.1 13.9 1.0 ND1 A:HIS241 2.2 12.0 1.0 CD A:GLU238 2.3 13.4 1.0 OE2 A:GLU238 2.4 13.5 1.0 OE2 A:GLU204 2.6 17.2 1.0 CD A:GLU115 2.9 13.5 1.0 OE1 A:GLU204 2.9 17.3 1.0 OE1 A:GLU115 3.0 13.8 1.0 CD A:GLU204 3.1 17.1 1.0 CE1 A:HIS241 3.1 12.0 1.0 CG A:HIS241 3.3 12.1 1.0 CB A:HIS241 3.6 12.2 1.0 FE A:FE376 3.6 24.1 1.0 NE1 A:TRP111 3.8 11.7 1.0 CE2 A:PHE208 3.8 16.4 1.0 CG A:GLU238 3.8 13.2 1.0 CG A:GLU115 4.2 13.1 1.0 NE2 A:HIS241 4.3 12.0 1.0 CD1 A:TRP111 4.3 11.6 1.0 CA A:GLU238 4.3 12.7 1.0 CD2 A:PHE208 4.4 16.3 1.0 CD2 A:HIS241 4.4 12.0 1.0 CB A:GLU238 4.5 12.9 1.0 CZ A:PHE208 4.6 16.4 1.0 CG A:GLU204 4.6 16.9 1.0 OD1 A:ASP84 4.9 13.9 1.0 CE1 A:HIS118 4.9 11.4 1.0 CE2 A:TRP111 4.9 11.7 1.0 N A:GLU238 5.0 12.6 1.0

Iron binding site 3 out of 4 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe376 b:27.7 occ:1.00 OD1 B:ASP84 1.9 14.8 1.0 ND1 B:HIS118 2.1 12.2 1.0 OE2 B:GLU115 2.2 13.8 1.0 OE2 B:GLU238 2.3 14.7 1.0 CG B:ASP84 2.7 14.4 1.0 OD2 B:ASP84 2.7 14.7 1.0 CE1 B:HIS118 2.8 12.2 1.0 CD B:GLU115 3.2 13.5 1.0 CG B:HIS118 3.3 12.2 1.0 CD B:GLU238 3.4 14.5 1.0 CZ B:PHE208 3.4 17.8 1.0 FE B:FE377 3.6 23.8 1.0 OE1 B:GLU115 3.7 13.8 1.0 CB B:HIS118 3.8 12.2 1.0 CE2 B:PHE208 4.0 17.8 1.0 NE2 B:HIS118 4.0 12.2 1.0 CE1 B:PHE208 4.1 17.8 1.0 OE1 B:GLU238 4.1 14.7 1.0 CB B:ASP84 4.1 14.3 1.0 CG B:GLU238 4.2 14.2 1.0 CG2 B:ILE234 4.2 12.8 1.0 CD2 B:HIS118 4.3 12.2 1.0 CA B:GLU115 4.4 12.5 1.0 CG B:GLU115 4.4 13.2 1.0 CB B:GLU115 4.5 12.7 1.0 CE1 B:HIS241 4.7 13.2 1.0 CA B:ASP84 4.8 14.0 1.0 ND1 B:HIS241 4.8 13.2 1.0 OH B:TYR122 4.9 14.6 1.0

Iron binding site 4 out of 4 in the Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleotide Reductase R2 Soaked with Ferrous Ion at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe377 b:23.8 occ:1.00 OE1 B:GLU238 1.8 14.7 1.0 OE1 B:GLU115 2.1 13.8 1.0 ND1 B:HIS241 2.2 13.2 1.0 OE2 B:GLU238 2.3 14.7 1.0 CD B:GLU238 2.4 14.5 1.0 OE2 B:GLU204 2.5 19.7 1.0 OE1 B:GLU204 2.6 19.8 1.0 CD B:GLU204 2.9 19.5 1.0 CD B:GLU115 2.9 13.5 1.0 CE1 B:HIS241 3.1 13.2 1.0 OE2 B:GLU115 3.1 13.8 1.0 CG B:HIS241 3.3 13.3 1.0 CB B:HIS241 3.6 13.5 1.0 FE B:FE376 3.6 27.7 1.0 CE2 B:PHE208 3.8 17.8 1.0 NE1 B:TRP111 3.8 11.8 1.0 CG B:GLU238 3.8 14.2 1.0 NE2 B:HIS241 4.2 13.2 1.0 CG B:GLU115 4.3 13.2 1.0 CD1 B:TRP111 4.3 11.8 1.0 CD2 B:HIS241 4.3 13.3 1.0 CA B:GLU238 4.4 13.4 1.0 CD2 B:PHE208 4.4 17.6 1.0 CG B:GLU204 4.4 19.3 1.0 CZ B:PHE208 4.5 17.8 1.0 CB B:GLU238 4.5 13.7 1.0 OD1 B:ASP84 4.7 14.8 1.0 CE1 B:HIS118 4.9 12.2 1.0 CE2 B:TRP111 5.0 11.8 1.0

W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollinger Jr., A.C.Rosenzweig. Variable Coordination Geometries at the Diiron(II) Active Site of Ribonucleotide Reductase R2. J.Am.Chem.Soc. V. 125 15822 2003.
ISSN: ISSN 0002-7863
PubMed: 14677973
DOI: 10.1021/JA0370387