Iron in PDB 6w4x: Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp

All present enzymatic activity of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp:
1.17.4.1;

The structure of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Iron atom in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp (pdb code 6w4x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp, PDB code: 6w4x:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:43.5 occ:1.00 FE1 C:FEO501 0.0 43.5 1.0 OE2 C:GLU115 1.7 37.5 1.0 O C:FEO501 1.8 43.5 1.0 OE1 C:GLU204 1.9 44.7 1.0 OE1 C:GLU238 2.2 39.7 1.0 ND1 C:HIS241 2.4 38.3 1.0 O C:HOH601 2.6 41.7 1.0 CD C:GLU115 2.6 37.5 1.0 OE1 C:GLU115 2.9 37.5 1.0 CD C:GLU238 2.9 39.7 1.0 FE2 C:FEO501 3.1 43.5 1.0 OE2 C:GLU238 3.1 39.7 1.0 CD C:GLU204 3.2 44.7 1.0 CE1 C:HIS241 3.2 38.3 1.0 CG C:HIS241 3.6 38.3 1.0 CG C:GLU115 4.0 37.5 1.0 OE2 C:GLU204 4.0 44.7 1.0 CB C:HIS241 4.0 38.3 1.0 CG C:GLU204 4.1 44.7 1.0 O C:HOH602 4.2 38.5 1.0 CG C:GLU238 4.3 39.7 1.0 NE1 C:TRP111 4.3 39.9 1.0 ND1 C:HIS118 4.4 33.7 1.0 NE2 C:HIS241 4.4 38.3 1.0 CE1 C:HIS118 4.5 33.7 1.0 CA C:GLU238 4.6 39.7 1.0 CD2 C:HIS241 4.6 38.3 1.0 CB C:GLU238 4.7 39.7 1.0 CD1 C:TRP111 4.8 39.9 1.0 OD1 C:ASP84 4.8 43.1 1.0 OE1 C:GLN87 5.0 44.1 1.0

Iron binding site 2 out of 4 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:43.5 occ:1.00 FE2 C:FEO501 0.0 43.5 1.0 O C:FEO501 1.8 43.5 1.0 OE1 C:GLU115 2.0 37.5 1.0 OD2 C:ASP84 2.2 43.1 1.0 ND1 C:HIS118 2.5 33.7 1.0 O C:HOH602 2.7 38.5 1.0 O C:HOH601 2.8 41.7 1.0 CG C:ASP84 2.8 43.1 1.0 OD1 C:ASP84 3.0 43.1 1.0 CD C:GLU115 3.0 37.5 1.0 FE1 C:FEO501 3.1 43.5 1.0 OE1 C:GLU238 3.2 39.7 1.0 CG C:HIS118 3.4 33.7 1.0 OE2 C:GLU115 3.4 37.5 1.0 CB C:HIS118 3.5 33.7 1.0 CE1 C:HIS118 3.5 33.7 1.0 F5 C:FY3122 3.8 38.8 1.0 CD C:GLU238 4.2 39.7 1.0 CB C:ASP84 4.2 43.1 1.0 CE2 C:PHE208 4.3 43.9 1.0 CG C:GLU115 4.3 37.5 1.0 CA C:GLU115 4.4 37.5 1.0 OE2 C:GLU238 4.5 39.7 1.0 CD2 C:HIS118 4.5 33.7 1.0 CB C:GLU115 4.6 37.5 1.0 NE2 C:HIS118 4.6 33.7 1.0 CD2 C:PHE208 4.7 43.9 1.0 OE1 C:GLU204 4.7 44.7 1.0 CE1 C:HIS241 4.8 38.3 1.0 ND1 C:HIS241 4.8 38.3 1.0 CA C:HIS118 5.0 33.7 1.0

Iron binding site 3 out of 4 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:62.5 occ:1.00 FE1 D:FEO501 0.0 62.5 1.0 OE1 D:GLU238 1.7 59.4 1.0 O D:FEO501 1.8 62.5 1.0 OE2 D:GLU115 1.9 51.7 1.0 OE1 D:GLU204 2.2 67.1 1.0 ND1 D:HIS241 2.4 52.5 1.0 CD D:GLU238 2.5 59.4 1.0 O D:HOH602 2.6 62.3 1.0 CD D:GLU115 2.7 51.7 1.0 OE1 D:GLU115 2.9 51.7 1.0 OE2 D:GLU238 3.0 59.4 1.0 CD D:GLU204 3.0 67.1 1.0 OE2 D:GLU204 3.1 67.1 1.0 FE2 D:FEO501 3.1 62.5 1.0 CE1 D:HIS241 3.2 52.5 1.0 CG D:HIS241 3.5 52.5 1.0 CG D:GLU238 3.8 59.4 1.0 NE1 D:TRP111 3.9 47.8 1.0 CB D:HIS241 3.9 52.5 1.0 CG D:GLU115 4.1 51.7 1.0 CE1 D:HIS118 4.3 51.8 1.0 ND1 D:HIS118 4.3 51.8 1.0 NE2 D:HIS241 4.4 52.5 1.0 OD1 D:ASP84 4.4 65.3 1.0 CG D:GLU204 4.4 67.1 1.0 CA D:GLU238 4.4 59.4 1.0 CB D:GLU238 4.5 59.4 1.0 CD1 D:TRP111 4.5 47.8 1.0 CD2 D:HIS241 4.6 52.5 1.0 O D:HOH601 4.7 65.3 1.0

Iron binding site 4 out of 4 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:62.5 occ:1.00 FE2 D:FEO501 0.0 62.5 1.0 O D:FEO501 1.8 62.5 1.0 OE1 D:GLU115 2.1 51.7 1.0 ND1 D:HIS118 2.1 51.8 1.0 OD1 D:ASP84 2.4 65.3 1.0 OD2 D:ASP84 2.5 65.3 1.0 O D:HOH601 2.6 65.3 1.0 O D:HOH602 2.7 62.3 1.0 OE2 D:GLU238 2.7 59.4 1.0 CG D:ASP84 2.7 65.3 1.0 CE1 D:HIS118 2.9 51.8 1.0 FE1 D:FEO501 3.1 62.5 1.0 CD D:GLU115 3.1 51.7 1.0 CD D:GLU238 3.1 59.4 1.0 CG D:HIS118 3.2 51.8 1.0 OE1 D:GLU238 3.5 59.4 1.0 OE2 D:GLU115 3.6 51.7 1.0 CB D:HIS118 3.6 51.8 1.0 CG D:GLU238 4.0 59.4 1.0 NE2 D:HIS118 4.1 51.8 1.0 CB D:ASP84 4.2 65.3 1.0 CD2 D:HIS118 4.2 51.8 1.0 CZ D:PHE208 4.2 76.0 1.0 F5 D:FY3122 4.4 62.9 1.0 CG D:GLU115 4.4 51.7 1.0 CA D:GLU115 4.5 51.7 1.0 CE1 D:PHE208 4.5 76.0 1.0 CB D:GLU115 4.6 51.7 1.0 CE2 D:PHE208 4.6 76.0 1.0 OE2 D:GLU204 4.8 67.1 1.0 CG2 D:ILE234 4.9 58.1 1.0 ND1 D:HIS241 4.9 52.5 1.0 CA D:ASP84 5.0 65.3 1.0 CE1 D:HIS241 5.0 52.5 1.0

G.Kang, A.T.Taguchi, J.Stubbe, C.L.Drennan. Structure of A Trapped Radical Transfer Pathway Within A Ribonucleotide Reductase Holocomplex. Science 2020.
ISSN: ESSN 1095-9203
PubMed: 32217749
DOI: 10.1126/SCIENCE.ABA6794