Iron in PDB 1pfr: Ribonucleoside-Diphosphate Reductase 1 Beta Chain

All present enzymatic activity of Ribonucleoside-Diphosphate Reductase 1 Beta Chain:
1.17.4.1;

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain, PDB code: 1pfr was solved by D.T.Logan, X.D.Su, A.Aberg, K.Regnstrom, J.Hajdu, H.Eklund, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.300, 85.500, 115.700, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / n/a

The structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain also contains other interesting chemical elements:

Mercury

(Hg)

8 atoms

The binding sites of Iron atom in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain (pdb code 1pfr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain, PDB code: 1pfr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:33.4 occ:1.00 OD1 A:ASP84 2.1 29.4 1.0 OE1 A:GLU115 2.2 16.7 1.0 OE2 A:GLU238 2.3 39.7 1.0 ND1 A:HIS118 2.4 14.2 1.0 CG A:ASP84 2.8 26.1 1.0 OD2 A:ASP84 2.9 30.9 1.0 CD A:GLU115 3.2 32.3 1.0 CD A:GLU238 3.2 44.6 1.0 CE1 A:HIS118 3.3 13.0 1.0 CG A:HIS118 3.4 12.9 1.0 OE1 A:GLU238 3.5 26.8 1.0 OE2 A:GLU115 3.7 30.4 1.0 CB A:HIS118 3.7 10.7 1.0 FE A:FE502 3.9 33.0 1.0 CZ A:PHE208 4.0 36.4 1.0 CB A:ASP84 4.2 15.1 1.0 CA A:GLU115 4.3 9.9 1.0 CG A:GLU115 4.3 19.7 1.0 CB A:GLU115 4.3 10.7 1.0 NE2 A:HIS118 4.4 13.3 1.0 CG A:GLU238 4.5 30.3 1.0 CD2 A:HIS118 4.5 13.6 1.0 CE1 A:PHE208 4.6 36.3 1.0 CE2 A:PHE208 4.6 37.9 1.0 CA A:ASP84 4.8 13.9 1.0 O A:GLU115 4.8 16.6 1.0 CG2 A:ILE234 4.9 17.5 1.0 OH A:TYR122 5.0 31.5 1.0

Iron binding site 2 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:33.0 occ:1.00 OE1 A:GLU238 1.9 26.8 1.0 OE2 A:GLU115 2.2 30.4 1.0 ND1 A:HIS241 2.4 19.9 1.0 OE2 A:GLU204 2.5 31.0 1.0 OE1 A:GLU204 2.5 34.3 1.0 CD A:GLU204 2.8 38.8 1.0 CD A:GLU115 2.9 32.3 1.0 CD A:GLU238 2.9 44.6 1.0 OE1 A:GLU115 3.0 16.7 1.0 CE1 A:HIS241 3.3 19.5 1.0 OE2 A:GLU238 3.4 39.7 1.0 CG A:HIS241 3.4 17.9 1.0 CB A:HIS241 3.7 14.2 1.0 NE1 A:TRP111 3.8 15.2 1.0 FE A:FE501 3.9 33.4 1.0 CG A:GLU238 4.3 30.3 1.0 CG A:GLU115 4.3 19.7 1.0 CG A:GLU204 4.4 26.8 1.0 CA A:GLU238 4.4 16.2 1.0 CD1 A:TRP111 4.4 16.4 1.0 NE2 A:HIS241 4.5 19.8 1.0 CD2 A:HIS241 4.5 19.6 1.0 CB A:GLU238 4.5 17.9 1.0 CE2 A:PHE208 4.6 37.9 1.0 NE2 A:GLN87 4.9 16.9 1.0 CE2 A:TRP111 5.0 16.1 1.0

Iron binding site 3 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe503 b:26.6 occ:1.00 ND1 B:HIS118 2.1 14.6 1.0 OD2 B:ASP84 2.1 24.0 1.0 OE1 B:GLU115 2.1 23.8 1.0 OE2 B:GLU238 2.2 25.5 1.0 OD1 B:ASP84 2.6 25.4 1.0 CG B:ASP84 2.7 23.0 1.0 CE1 B:HIS118 3.0 14.0 1.0 CG B:HIS118 3.2 12.8 1.0 O B:HOH663 3.3 23.7 1.0 CD B:GLU115 3.3 28.4 1.0 CD B:GLU238 3.4 46.6 1.0 FE B:FE504 3.5 26.9 1.0 CB B:HIS118 3.6 9.7 1.0 OE2 B:GLU115 3.8 35.9 1.0 OE1 B:GLU238 4.1 51.0 1.0 NE2 B:HIS118 4.1 14.5 1.0 CB B:ASP84 4.2 16.0 1.0 CD2 B:HIS118 4.2 14.5 1.0 CB B:GLU115 4.4 9.8 1.0 CG B:GLU115 4.4 16.5 1.0 CZ B:PHE208 4.5 29.7 1.0 CG B:GLU238 4.5 26.8 1.0 CA B:GLU115 4.5 8.5 1.0 CG2 B:ILE234 4.5 12.1 1.0 CE2 B:PHE208 4.6 30.7 1.0 CE1 B:HIS241 5.0 11.8 1.0 CE1 B:PHE208 5.0 30.9 1.0 ND1 B:HIS241 5.0 12.9 1.0

Iron binding site 4 out of 4 in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ribonucleoside-Diphosphate Reductase 1 Beta Chain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe504 b:26.9 occ:1.00 OE1 B:GLU238 1.5 51.0 1.0 OE2 B:GLU115 2.2 35.9 1.0 CD B:GLU238 2.2 46.6 1.0 OE2 B:GLU238 2.4 25.5 1.0 ND1 B:HIS241 2.4 12.9 1.0 O B:HOH663 2.5 23.7 1.0 OE2 B:GLU204 2.5 34.8 1.0 OE1 B:GLU115 2.9 23.8 1.0 CD B:GLU115 2.9 28.4 1.0 OE1 B:GLU204 3.1 55.5 1.0 CD B:GLU204 3.1 45.3 1.0 CE1 B:HIS241 3.3 11.8 1.0 CG B:HIS241 3.5 12.5 1.0 FE B:FE503 3.5 26.6 1.0 CG B:GLU238 3.7 26.8 1.0 CB B:HIS241 3.8 10.8 1.0 NE1 B:TRP111 4.1 11.4 1.0 CG B:GLU115 4.3 16.5 1.0 OD1 B:ASP84 4.4 25.4 1.0 NE2 B:HIS241 4.5 12.6 1.0 CA B:GLU238 4.5 14.4 1.0 CG B:GLU204 4.5 30.3 1.0 CD2 B:HIS241 4.6 13.5 1.0 CB B:GLU238 4.6 15.3 1.0 CD1 B:TRP111 4.7 12.3 1.0 CE1 B:HIS118 4.8 14.0 1.0 ND1 B:HIS118 4.8 14.6 1.0 NE2 B:GLN87 4.9 13.3 1.0

D.T.Logan, X.D.Su, A.Aberg, K.Regnstrom, J.Hajdu, H.Eklund, P.Nordlund. Crystal Structure of Reduced Protein R2 of Ribonucleotide Reductase: the Structural Basis For Oxygen Activation at A Dinuclear Iron Site. Structure V. 4 1053 1996.
ISSN: ISSN 0969-2126
PubMed: 8805591
DOI: 10.1016/S0969-2126(96)00112-8