Iron in PDB 1xik: 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: 1xik 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.440, 83.530, 113.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 28

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

Mercury

(Hg)

10 atoms

The binding sites of Iron atom in the Ribonucleoside-Diphosphate Reductase 1 Beta Chain (pdb code 1xik). 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: 1xik:
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:Fe376 b:17.0 occ:1.00 OD1 A:ASP84 1.7 20.6 1.0 OE2 A:GLU238 1.7 29.7 1.0 OE1 A:GLU115 2.0 24.4 1.0 ND1 A:HIS118 2.0 18.2 1.0 CG A:ASP84 2.5 20.9 1.0 OD2 A:ASP84 2.7 21.6 1.0 CD A:GLU238 2.8 36.0 1.0 CE1 A:HIS118 2.8 18.2 1.0 CD A:GLU115 3.1 28.3 1.0 CG A:HIS118 3.1 17.4 1.0 OE1 A:GLU238 3.4 25.3 1.0 CZ A:PHE208 3.6 31.0 1.0 CB A:HIS118 3.6 15.6 1.0 OE2 A:GLU115 3.7 23.3 1.0 FE A:FE2377 3.9 19.7 1.0 CB A:ASP84 4.0 18.9 1.0 NE2 A:HIS118 4.0 18.4 1.0 CE2 A:PHE208 4.1 32.9 1.0 CG A:GLU238 4.1 27.8 1.0 CE1 A:PHE208 4.1 31.6 1.0 CD2 A:HIS118 4.2 18.4 1.0 CA A:GLU115 4.2 15.6 1.0 CG A:GLU115 4.3 18.1 1.0 CB A:GLU115 4.3 16.2 1.0 CG2 A:ILE234 4.3 18.4 1.0 CA A:ASP84 4.8 18.1 1.0 OH A:TYR122 4.8 27.4 1.0 O A:GLU115 4.9 19.0 1.0 CE1 A:HIS241 4.9 23.1 1.0 ND1 A:HIS241 4.9 23.4 1.0 CD2 A:PHE208 5.0 29.6 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:Fe377 b:19.7 occ:1.00 OE1 A:GLU238 1.8 25.3 1.0 OE2 A:GLU115 2.0 23.3 1.0 ND1 A:HIS241 2.0 23.4 1.0 OE1 A:GLU204 2.2 25.4 1.0 CD A:GLU115 2.8 28.3 1.0 CD A:GLU204 2.9 40.7 1.0 CD A:GLU238 2.9 36.0 1.0 OE2 A:GLU204 2.9 29.8 1.0 OE1 A:GLU115 3.0 24.4 1.0 CE1 A:HIS241 3.0 23.1 1.0 CG A:HIS241 3.0 21.6 1.0 CB A:HIS241 3.4 17.9 1.0 OE2 A:GLU238 3.5 29.7 1.0 NE1 A:TRP111 3.7 21.2 1.0 FE A:FE2376 3.9 17.0 1.0 CE2 A:PHE208 4.0 32.9 1.0 CG A:GLU115 4.1 18.1 1.0 NE2 A:HIS241 4.1 23.3 1.0 CG A:GLU238 4.1 27.8 1.0 CA A:GLU238 4.1 20.4 1.0 CD2 A:HIS241 4.2 23.7 1.0 CD1 A:TRP111 4.2 21.6 1.0 CB A:GLU238 4.2 21.1 1.0 CG A:GLU204 4.3 32.0 1.0 CD2 A:PHE208 4.7 29.6 1.0 OD1 A:ASP84 4.7 20.6 1.0 CZ A:PHE208 4.8 31.0 1.0 CB A:GLU204 4.8 25.5 1.0 CE2 A:TRP111 4.9 22.1 1.0 N A:GLU238 4.9 21.3 1.0 CA A:HIS241 4.9 17.2 1.0 O A:GLU238 5.0 22.9 1.0 CE1 A:HIS118 5.0 18.2 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:Fe376 b:20.9 occ:1.00 OE2 B:GLU238 1.8 45.2 1.0 OD1 B:ASP84 2.0 24.3 1.0 ND1 B:HIS118 2.1 16.3 1.0 OE1 B:GLU115 2.2 21.2 1.0 CG B:ASP84 2.7 22.4 1.0 OD2 B:ASP84 2.7 27.6 1.0 CE1 B:HIS118 2.8 15.7 1.0 CD B:GLU238 2.9 40.5 1.0 CD B:GLU115 3.1 27.9 1.0 CG B:HIS118 3.2 15.3 1.0 OE1 B:GLU238 3.3 30.7 1.0 CZ B:PHE208 3.5 29.6 1.0 OE2 B:GLU115 3.7 28.2 1.0 CB B:HIS118 3.8 14.0 1.0 FE B:FE2377 3.9 26.2 1.0 CE2 B:PHE208 3.9 32.3 1.0 NE2 B:HIS118 4.1 16.2 1.0 CB B:ASP84 4.1 16.5 1.0 CG B:GLU238 4.2 28.4 1.0 CE1 B:PHE208 4.2 30.5 1.0 CD2 B:HIS118 4.3 16.6 1.0 CA B:GLU115 4.3 12.9 1.0 CG B:GLU115 4.3 15.1 1.0 CB B:GLU115 4.3 13.5 1.0 CG2 B:ILE234 4.4 16.7 1.0 CE1 B:HIS241 4.7 14.7 1.0 CA B:ASP84 4.8 15.3 1.0 ND1 B:HIS241 4.8 15.5 1.0 CD2 B:PHE208 4.9 29.7 1.0 O B:GLU115 4.9 18.8 1.0 OH B:TYR122 4.9 26.3 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:Fe377 b:26.2 occ:1.00 OE1 B:GLU238 1.8 30.7 1.0 ND1 B:HIS241 2.0 15.5 1.0 OE2 B:GLU115 2.1 28.2 1.0 OE1 B:GLU204 2.4 45.2 1.0 OE2 B:GLU204 2.5 32.6 1.0 CD B:GLU204 2.8 35.4 1.0 CD B:GLU115 2.8 27.9 1.0 CD B:GLU238 3.0 40.5 1.0 OE1 B:GLU115 3.0 21.2 1.0 CE1 B:HIS241 3.0 14.7 1.0 CG B:HIS241 3.0 14.8 1.0 CB B:HIS241 3.4 13.1 1.0 OE2 B:GLU238 3.5 45.2 1.0 NE1 B:TRP111 3.7 18.2 1.0 FE B:FE2376 3.9 20.9 1.0 NE2 B:HIS241 4.1 14.6 1.0 CD2 B:HIS241 4.2 15.2 1.0 CG B:GLU238 4.2 28.4 1.0 CD1 B:TRP111 4.2 18.7 1.0 CG B:GLU115 4.3 15.1 1.0 CA B:GLU238 4.3 17.5 1.0 CG B:GLU204 4.3 29.5 1.0 CB B:GLU238 4.4 18.6 1.0 CE2 B:PHE208 4.4 32.3 1.0 CE2 B:TRP111 4.8 19.4 1.0 CD2 B:PHE208 4.8 29.7 1.0 OD1 B:ASP84 4.9 24.3 1.0 CA B:HIS241 4.9 13.3 1.0 N B:GLU238 4.9 18.6 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