Iron in PDB 6n2o: 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound

The structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound, PDB code: 6n2o was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.01 / 2.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.407, 100.532, 202.053, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.1

The structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound (pdb code 6n2o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound, PDB code: 6n2o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:43.0 occ:1.00 FE1 B:SF4401 0.0 43.0 1.0 S2 B:SF4401 2.3 40.1 1.0 S4 B:SF4401 2.3 42.6 1.0 S3 B:SF4401 2.3 43.9 1.0 SG B:CYS209 2.3 43.3 1.0 FE3 B:SF4401 2.7 39.3 1.0 FE4 B:SF4401 2.7 40.2 1.0 FE2 B:SF4401 2.7 39.4 1.0 CB B:CYS209 3.4 44.7 1.0 S1 B:SF4401 3.9 38.8 1.0 CA B:CYS209 4.1 45.4 1.0 CB B:THR211 4.4 43.9 1.0 CD2 B:PHE212 4.5 46.5 1.0 CA B:GLY134 4.6 42.3 1.0 C B:CYS209 4.6 47.9 1.0 OG1 B:THR211 4.7 44.0 1.0 SG B:CYS60 4.8 43.2 1.0 N B:THR211 4.8 45.0 1.0 SG B:CYS29 4.8 44.7 1.0 SG B:CYS26 4.9 45.6 1.0 ND2 B:ASN130 5.0 40.9 1.0

Iron binding site 2 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:39.4 occ:1.00 FE2 B:SF4401 0.0 39.4 1.0 S3 B:SF4401 2.3 43.9 1.0 S4 B:SF4401 2.3 42.6 1.0 S1 B:SF4401 2.3 38.8 1.0 SG B:CYS29 2.3 44.7 1.0 FE4 B:SF4401 2.7 40.2 1.0 FE3 B:SF4401 2.7 39.3 1.0 FE1 B:SF4401 2.7 43.0 1.0 CB B:CYS29 3.0 42.3 1.0 S2 B:SF4401 3.9 40.1 1.0 CA B:CYS29 4.2 43.6 1.0 CD2 B:HIS31 4.4 44.6 1.0 SG B:CYS209 4.5 43.3 1.0 SG B:CYS26 4.7 45.6 1.0 N B:CYS26 4.7 43.3 1.0 NE2 B:HIS31 4.8 43.5 1.0 CB B:CYS60 4.8 40.1 1.0 SG B:CYS60 4.8 43.2 1.0 CB B:CYS209 4.8 44.7 1.0 O B:GLN208 4.9 44.7 1.0 CA B:CYS209 4.9 45.4 1.0 CB B:TRP25 4.9 41.5 1.0 CB B:CYS26 4.9 42.0 1.0 CD1 B:TRP25 4.9 43.0 1.0 CG B:HIS31 4.9 44.6 1.0 CG B:TRP25 5.0 42.0 1.0

Iron binding site 3 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:39.3 occ:1.00 FE3 B:SF4401 0.0 39.3 1.0 S4 B:SF4401 2.3 42.6 1.0 S2 B:SF4401 2.3 40.1 1.0 S1 B:SF4401 2.3 38.8 1.0 SG B:CYS60 2.3 43.2 1.0 FE1 B:SF4401 2.7 43.0 1.0 FE2 B:SF4401 2.7 39.4 1.0 FE4 B:SF4401 2.7 40.2 1.0 CB B:CYS60 3.1 40.1 1.0 S3 B:SF4401 3.9 43.9 1.0 CA B:GLY134 4.5 42.3 1.0 CA B:CYS60 4.5 41.4 1.0 C B:GLY134 4.6 40.7 1.0 SG B:CYS29 4.8 44.7 1.0 N B:LEU135 4.8 40.1 1.0 SG B:CYS26 4.8 45.6 1.0 SG B:CYS209 4.9 43.3 1.0 CD1 A:ILE46 4.9 45.4 1.0 O3B B:TPP402 4.9 39.8 1.0 O B:GLY134 5.0 40.1 1.0 CD1 B:TRP25 5.0 43.0 1.0

Iron binding site 4 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:40.2 occ:1.00 FE4 B:SF4401 0.0 40.2 1.0 S1 B:SF4401 2.3 38.8 1.0 S3 B:SF4401 2.3 43.9 1.0 S2 B:SF4401 2.3 40.1 1.0 SG B:CYS26 2.3 45.6 1.0 FE2 B:SF4401 2.7 39.4 1.0 FE1 B:SF4401 2.7 43.0 1.0 FE3 B:SF4401 2.7 39.3 1.0 CB B:CYS26 3.3 42.0 1.0 OG1 B:THR211 3.8 44.0 1.0 S4 B:SF4401 3.9 42.6 1.0 N B:CYS26 3.9 43.3 1.0 CB B:THR211 4.2 43.9 1.0 CA B:CYS26 4.2 42.8 1.0 CG2 A:ILE46 4.6 44.2 1.0 CB B:CYS29 4.7 42.3 1.0 SG B:CYS29 4.8 44.7 1.0 SG B:CYS60 4.8 43.2 1.0 SG B:CYS209 4.8 43.3 1.0 CG2 B:THR211 4.9 39.9 1.0 CB A:ILE46 5.0 43.4 1.0

Iron binding site 5 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:50.1 occ:1.00 FE1 D:SF4401 0.0 50.1 1.0 S2 D:SF4401 2.3 51.4 1.0 S4 D:SF4401 2.3 53.3 1.0 S3 D:SF4401 2.3 54.1 1.0 SG D:CYS209 2.3 52.1 1.0 FE3 D:SF4401 2.7 52.0 1.0 FE4 D:SF4401 2.7 61.7 1.0 FE2 D:SF4401 2.7 54.6 1.0 CB D:CYS209 3.5 55.5 1.0 S1 D:SF4401 3.9 52.7 1.0 CA D:CYS209 4.0 58.5 1.0 CB D:THR211 4.3 55.0 1.0 CD2 D:PHE212 4.5 53.8 1.0 OG1 D:THR211 4.5 55.9 1.0 CA D:GLY134 4.5 51.4 1.0 C D:CYS209 4.6 58.2 1.0 N D:THR211 4.7 53.6 1.0 SG D:CYS29 4.8 59.6 1.0 SG D:CYS26 4.9 60.2 1.0 SG D:CYS60 4.9 56.0 1.0

Iron binding site 6 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:54.6 occ:1.00 FE2 D:SF4401 0.0 54.6 1.0 S1 D:SF4401 2.3 52.7 1.0 SG D:CYS29 2.3 59.6 1.0 S3 D:SF4401 2.3 54.1 1.0 S4 D:SF4401 2.3 53.3 1.0 FE4 D:SF4401 2.7 61.7 1.0 FE3 D:SF4401 2.7 52.0 1.0 FE1 D:SF4401 2.7 50.1 1.0 CB D:CYS29 3.0 58.1 1.0 S2 D:SF4401 3.9 51.4 1.0 CA D:CYS29 4.2 55.7 1.0 CD2 D:HIS31 4.3 54.4 1.0 NE2 D:HIS31 4.6 55.2 1.0 SG D:CYS209 4.6 52.1 1.0 CB D:CYS60 4.7 52.2 1.0 SG D:CYS26 4.8 60.2 1.0 N D:CYS26 4.8 57.7 1.0 SG D:CYS60 4.8 56.0 1.0 CG D:HIS31 4.8 55.4 1.0 O D:GLN208 4.8 57.7 1.0 CB D:CYS209 4.9 55.5 1.0 CB D:TRP25 4.9 53.0 1.0 CA D:CYS209 4.9 58.5 1.0 CB D:CYS26 4.9 60.2 1.0

Iron binding site 7 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:52.0 occ:1.00 FE3 D:SF4401 0.0 52.0 1.0 S4 D:SF4401 2.3 53.3 1.0 S2 D:SF4401 2.3 51.4 1.0 S1 D:SF4401 2.3 52.7 1.0 SG D:CYS60 2.3 56.0 1.0 FE2 D:SF4401 2.7 54.6 1.0 FE4 D:SF4401 2.7 61.7 1.0 FE1 D:SF4401 2.7 50.1 1.0 CB D:CYS60 3.0 52.2 1.0 S3 D:SF4401 3.9 54.1 1.0 C D:GLY134 4.5 52.1 1.0 CA D:GLY134 4.5 51.4 1.0 CA D:CYS60 4.5 53.0 1.0 CG1 C:ILE46 4.6 65.1 1.0 N D:LEU135 4.6 51.1 1.0 SG D:CYS26 4.7 60.2 1.0 O3B D:TPP402 4.8 50.3 1.0 SG D:CYS29 4.8 59.6 1.0 SG D:CYS209 4.9 52.1 1.0 O D:GLY134 4.9 51.2 1.0

Iron binding site 8 out of 8 in the 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus with 2-Oxoglutarate, Coenzyme A and Succinyl-Coa Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:61.7 occ:1.00 FE4 D:SF4401 0.0 61.7 1.0 S1 D:SF4401 2.3 52.7 1.0 SG D:CYS26 2.3 60.2 1.0 S3 D:SF4401 2.3 54.1 1.0 S2 D:SF4401 2.3 51.4 1.0 FE2 D:SF4401 2.7 54.6 1.0 FE3 D:SF4401 2.7 52.0 1.0 FE1 D:SF4401 2.7 50.1 1.0 CB D:CYS26 3.2 60.2 1.0 OG1 D:THR211 3.6 55.9 1.0 N D:CYS26 3.8 57.7 1.0 S4 D:SF4401 3.9 53.3 1.0 CA D:CYS26 4.1 59.6 1.0 CB D:THR211 4.2 55.0 1.0 CG2 C:ILE46 4.5 64.4 1.0 CB D:CYS29 4.5 58.1 1.0 CB C:ILE46 4.5 67.0 1.0 SG D:CYS60 4.7 56.0 1.0 SG D:CYS29 4.7 59.6 1.0 SG D:CYS209 4.8 52.1 1.0 CG1 C:ILE46 4.9 65.1 1.0 C D:TRP25 4.9 56.7 1.0

P.Y.Chen, B.Li, C.L.Drennan, S.J.Elliott. A Reverse Tca Cycle 2-Oxoacid:Ferredoxin Oxidoreductase That Makes C-C Bonds From CO2. Joule V. 3 595 2019.
ISSN: ESSN 2542-4351
PubMed: 31080943
DOI: 10.1016/J.JOULE.2018.12.006