Iron in PDB 1pj1: Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5

All present enzymatic activity of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5:
1.17.4.1;

The structure of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5, PDB code: 1pj1 was solved by W.C.Voegtli, M.Sommerhalter, L.Saleh, J.Baldwin, J.M.Bollingerjr., A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.100, 84.200, 114.700, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.1

The structure of Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5 also contains other interesting chemical elements:

Mercury

(Hg)

15 atoms

The binding sites of Iron atom in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5 (pdb code 1pj1). 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-D84E/W48F Soaked with Ferrous Ions at pH 5, PDB code: 1pj1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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-D84E/W48F Soaked with Ferrous Ions at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe406 b:20.0 occ:1.00 OE2 A:GLU238 2.0 21.3 1.0 OE1 A:GLU115 2.1 14.9 1.0 ND1 A:HIS118 2.1 11.9 1.0 OE2 A:GLU84 2.2 16.6 1.0 OE1 A:GLU84 2.3 16.6 1.0 CD A:GLU84 2.5 16.4 1.0 CE1 A:HIS118 3.0 12.1 1.0 CG A:HIS118 3.2 12.8 1.0 CD A:GLU238 3.2 22.0 1.0 CD A:GLU115 3.2 16.1 1.0 CB A:HIS118 3.6 14.4 1.0 CZ A:PHE208 3.7 24.6 1.0 OE1 A:GLU238 3.7 22.1 1.0 OE2 A:GLU115 3.8 16.4 1.0 FE A:FE407 4.0 15.1 1.0 CG A:GLU84 4.0 14.6 1.0 CE2 A:PHE208 4.1 25.4 1.0 NE2 A:HIS118 4.2 13.8 1.0 CG2 A:ILE234 4.2 16.2 1.0 CA A:GLU115 4.2 15.0 1.0 CE1 A:PHE208 4.3 23.4 1.0 CD2 A:HIS118 4.3 12.5 1.0 CG A:GLU115 4.3 14.2 1.0 CB A:GLU115 4.4 15.1 1.0 CG A:GLU238 4.4 18.4 1.0 O A:HOH443 4.6 23.6 1.0 CE1 A:HIS241 4.7 13.0 1.0 CD2 A:PHE208 4.8 24.2 1.0 O A:GLU115 4.9 15.1 1.0 CB A:GLU84 4.9 14.5 1.0 ND1 A:HIS241 4.9 13.9 1.0

Iron binding site 2 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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-D84E/W48F Soaked with Ferrous Ions at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe407 b:15.1 occ:1.00 OE2 A:GLU115 2.0 16.4 1.0 OE1 A:GLU238 2.0 22.1 1.0 OE1 A:GLU204 2.0 25.0 1.0 ND1 A:HIS241 2.0 13.9 1.0 CD A:GLU204 2.8 20.4 1.0 CD A:GLU115 2.8 16.1 1.0 OE2 A:GLU204 2.9 20.6 1.0 CE1 A:HIS241 3.0 13.0 1.0 CD A:GLU238 3.0 22.0 1.0 OE1 A:GLU115 3.0 14.9 1.0 CG A:HIS241 3.1 13.7 1.0 OE2 A:GLU238 3.4 21.3 1.0 CB A:HIS241 3.4 12.9 1.0 NE1 A:TRP111 3.7 18.0 1.0 CE2 A:PHE208 3.8 25.4 1.0 FE A:FE406 4.0 20.0 1.0 NE2 A:HIS241 4.1 13.0 1.0 CG A:GLU115 4.2 14.2 1.0 CD1 A:TRP111 4.2 15.6 1.0 CD2 A:HIS241 4.2 13.2 1.0 CG A:GLU204 4.2 22.0 1.0 CA A:GLU238 4.3 18.4 1.0 CD2 A:PHE208 4.3 24.2 1.0 CG A:GLU238 4.3 18.4 1.0 CB A:GLU238 4.6 17.3 1.0 CZ A:PHE208 4.7 24.6 1.0 CB A:GLU204 4.8 20.9 1.0 CE2 A:TRP111 4.9 15.0 1.0 CA A:HIS241 5.0 13.9 1.0 N A:GLU238 5.0 17.6 1.0

Iron binding site 3 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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-D84E/W48F Soaked with Ferrous Ions at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe408 b:20.9 occ:1.00 OE1 B:GLU238 2.0 20.8 1.0 ND1 B:HIS118 2.1 15.4 1.0 OE1 B:GLU115 2.1 15.9 1.0 OE2 B:GLU84 2.1 16.9 1.0 OE1 B:GLU84 2.3 17.2 1.0 CD B:GLU84 2.5 18.8 1.0 CE1 B:HIS118 3.0 14.7 1.0 CD B:GLU238 3.1 19.8 1.0 CG B:HIS118 3.2 13.3 1.0 CD B:GLU115 3.2 15.0 1.0 OE2 B:GLU238 3.5 18.0 1.0 CB B:HIS118 3.6 14.8 1.0 CZ B:PHE208 3.7 26.8 1.0 OE2 B:GLU115 3.8 17.1 1.0 FE B:FE409 3.9 16.2 1.0 CG B:GLU84 4.0 18.0 1.0 CE2 B:PHE208 4.1 25.4 1.0 NE2 B:HIS118 4.1 15.7 1.0 CG2 B:ILE234 4.2 16.8 1.0 CA B:GLU115 4.2 15.0 1.0 CD2 B:HIS118 4.3 15.7 1.0 CE1 B:PHE208 4.3 24.7 1.0 CG B:GLU238 4.3 15.4 1.0 CG B:GLU115 4.4 14.4 1.0 CB B:GLU115 4.4 12.9 1.0 O B:HOH434 4.6 24.7 1.0 CE1 B:HIS241 4.7 13.0 1.0 ND1 B:HIS241 4.8 13.4 1.0 O B:GLU115 4.8 14.2 1.0 CB B:GLU84 4.9 16.4 1.0 CD2 B:PHE208 4.9 24.5 1.0

Iron binding site 4 out of 4 in the Ribonucleotide Reductase R2-D84E/W48F Soaked with Ferrous Ions at pH 5


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-D84E/W48F Soaked with Ferrous Ions at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe409 b:16.2 occ:1.00 OE2 B:GLU238 1.9 18.0 1.0 OE1 B:GLU204 2.0 23.7 1.0 OE2 B:GLU115 2.1 17.1 1.0 ND1 B:HIS241 2.1 13.4 1.0 CD B:GLU204 2.8 20.5 1.0 CD B:GLU115 2.8 15.0 1.0 OE2 B:GLU204 2.9 21.0 1.0 CD B:GLU238 3.0 19.8 1.0 OE1 B:GLU115 3.0 15.9 1.0 CE1 B:HIS241 3.0 13.0 1.0 CG B:HIS241 3.1 13.3 1.0 CB B:HIS241 3.4 13.1 1.0 OE1 B:GLU238 3.5 20.8 1.0 CE2 B:PHE208 3.7 25.4 1.0 NE1 B:TRP111 3.7 14.4 1.0 FE B:FE408 3.9 20.9 1.0 NE2 B:HIS241 4.2 10.9 1.0 CD1 B:TRP111 4.2 12.3 1.0 CG B:GLU115 4.2 14.4 1.0 CD2 B:HIS241 4.2 11.7 1.0 CG B:GLU204 4.2 20.1 1.0 CD2 B:PHE208 4.3 24.5 1.0 CA B:GLU238 4.3 14.8 1.0 CG B:GLU238 4.3 15.4 1.0 CB B:GLU238 4.5 15.0 1.0 CZ B:PHE208 4.5 26.8 1.0 CB B:GLU204 4.8 19.2 1.0 CE2 B:TRP111 4.9 15.0 1.0 CA B:HIS241 4.9 12.8 1.0 N B:GLU238 5.0 15.9 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