Magnesium 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:

Iron

(Fe)

8 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg403 b:42.9 occ:1.00 O2A B:TPP402 2.0 43.3 1.0 O B:HOH504 2.0 42.9 1.0 OD1 B:ASP102 2.1 42.4 1.0 OD1 B:ASN130 2.1 46.7 1.0 O1B B:TPP402 2.2 43.8 1.0 O B:ILE132 2.2 42.5 1.0 CG B:ASN130 3.0 43.9 1.0 PA B:TPP402 3.2 41.9 1.0 CG B:ASP102 3.2 43.2 1.0 ND2 B:ASN130 3.2 40.9 1.0 PB B:TPP402 3.3 42.5 1.0 O3A B:TPP402 3.4 45.5 1.0 C B:ILE132 3.5 43.9 1.0 OD2 B:ASP102 3.7 44.2 1.0 N B:ASP102 3.8 41.7 1.0 O2B B:TPP402 4.0 41.8 1.0 O7 B:TPP402 4.1 41.6 1.0 N B:ILE132 4.1 42.7 1.0 N B:GLY103 4.3 39.4 1.0 O1A B:TPP402 4.3 42.6 1.0 N B:TYR133 4.3 44.1 1.0 CB B:ASN130 4.3 42.9 1.0 N B:ASN130 4.3 42.5 1.0 CA B:TYR133 4.4 43.3 1.0 CA B:ILE132 4.4 45.2 1.0 CB B:ASP102 4.4 41.1 1.0 N B:GLY134 4.4 43.2 1.0 CA B:GLY101 4.5 39.5 1.0 O3B B:TPP402 4.5 39.8 1.0 O B:MET128 4.5 41.6 1.0 CA B:ASP102 4.6 41.1 1.0 C B:GLY101 4.6 40.4 1.0 N B:GLY131 4.7 46.0 1.0 CA B:ASN130 4.7 44.2 1.0 C B:ASN130 4.9 46.8 1.0 CG2 B:ILE132 4.9 43.9 1.0 C B:TYR133 4.9 43.1 1.0 C B:ASP102 5.0 41.1 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 D:Mg403 b:46.5 occ:1.00 OD1 D:ASN130 2.0 52.5 1.0 O1B D:TPP402 2.1 47.2 1.0 OD1 D:ASP102 2.1 47.1 1.0 O1A D:TPP402 2.1 49.3 1.0 O D:ILE132 2.2 47.5 1.0 O D:HOH502 2.4 48.6 1.0 CG D:ASN130 2.8 50.1 1.0 ND2 D:ASN130 3.0 51.9 1.0 CG D:ASP102 3.2 46.8 1.0 PB D:TPP402 3.3 54.4 1.0 PA D:TPP402 3.3 47.7 1.0 C D:ILE132 3.5 50.2 1.0 O3A D:TPP402 3.6 54.1 1.0 OD2 D:ASP102 3.6 46.4 1.0 N D:ASP102 4.0 47.1 1.0 O2B D:TPP402 4.0 54.9 1.0 N D:ILE132 4.2 48.0 1.0 N D:GLY134 4.2 51.8 1.0 O7 D:TPP402 4.2 49.7 1.0 CB D:ASN130 4.3 48.0 1.0 CA D:TYR133 4.3 50.7 1.0 N D:TYR133 4.3 47.9 1.0 N D:GLY103 4.4 44.8 1.0 O2A D:TPP402 4.4 51.8 1.0 O3B D:TPP402 4.4 50.3 1.0 CB D:ASP102 4.5 48.4 1.0 CA D:ILE132 4.5 49.7 1.0 N D:ASN130 4.5 51.9 1.0 CA D:GLY101 4.6 49.6 1.0 O D:MET128 4.7 50.4 1.0 CA D:ASP102 4.7 44.5 1.0 C D:TYR133 4.8 51.6 1.0 C D:GLY101 4.8 48.9 1.0 CA D:ASN130 4.8 48.8 1.0 N D:GLY131 4.8 49.5 1.0 CG2 D:ILE132 4.9 48.8 1.0 C D:ASN130 4.9 48.1 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