Iron in PDB 5b46: 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form, PDB code: 5b46 was solved by Z.Yan, A.Maruyama, T.Arakawa, S.Fushinobu, T.Wakagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.93 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	101.889, 205.048, 126.988, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.9

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form (pdb code 5b46). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form, PDB code: 5b46:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:38.9 occ:0.70 FE1 B:SF4401 0.0 38.9 0.7 S2 B:SF4401 2.1 45.1 0.7 S4 B:SF4401 2.1 40.8 0.7 S3 B:SF4401 2.1 41.6 0.7 SG B:CYS12 2.3 45.4 1.0 FE2 B:SF4401 2.8 35.8 0.7 FE4 B:SF4401 2.8 39.5 0.7 FE3 B:SF4401 2.9 37.3 0.7 CB B:CYS12 3.0 48.1 1.0 OG1 B:THR199 3.5 48.9 1.0 S1 B:SF4401 3.7 38.9 0.7 N B:CYS12 3.7 49.8 1.0 CA B:CYS12 4.0 48.3 1.0 CB B:THR199 4.1 54.1 1.0 O A:HOH822 4.1 46.5 1.0 CB A:ILE44 4.4 52.6 1.0 CG2 A:ILE44 4.6 52.6 1.0 CG1 A:ILE44 4.7 57.2 1.0 CB B:CYS15 4.8 50.0 1.0 SG B:CYS46 4.8 44.2 1.0 CG2 B:THR199 4.9 56.8 1.0 SG B:CYS15 4.9 51.1 1.0 SG B:CYS197 4.9 44.3 1.0 C B:TRP11 4.9 50.4 1.0

Iron binding site 2 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:35.8 occ:0.70 FE2 B:SF4401 0.0 35.8 0.7 S3 B:SF4401 2.1 41.6 0.7 S4 B:SF4401 2.2 40.8 0.7 S1 B:SF4401 2.2 38.9 0.7 SG B:CYS46 2.3 44.2 1.0 FE1 B:SF4401 2.8 38.9 0.7 FE4 B:SF4401 2.8 39.5 0.7 FE3 B:SF4401 2.9 37.3 0.7 CB B:CYS46 2.9 47.3 1.0 S2 B:SF4401 3.7 45.1 0.7 CA B:GLY122 4.1 46.3 1.0 C B:GLY122 4.3 48.0 1.0 CA B:CYS46 4.5 49.8 1.0 CG1 A:ILE44 4.5 57.2 1.0 N B:LEU123 4.7 46.0 1.0 O B:GLY122 4.8 41.4 1.0 SG B:CYS12 4.9 45.4 1.0 SG B:CYS197 4.9 44.3 1.0 SG B:CYS15 5.0 51.1 1.0

Iron binding site 3 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:37.3 occ:0.70 FE3 B:SF4401 0.0 37.3 0.7 S2 B:SF4401 2.1 45.1 0.7 S4 B:SF4401 2.1 40.8 0.7 S1 B:SF4401 2.2 38.9 0.7 SG B:CYS197 2.2 44.3 1.0 FE4 B:SF4401 2.9 39.5 0.7 FE1 B:SF4401 2.9 38.9 0.7 FE2 B:SF4401 2.9 35.8 0.7 CB B:CYS197 3.1 50.1 1.0 CA B:CYS197 3.6 52.2 1.0 S3 B:SF4401 3.8 41.6 0.7 C B:CYS197 4.2 51.0 1.0 CB B:THR199 4.3 54.1 1.0 CA B:GLY122 4.5 46.3 1.0 CD2 B:TYR200 4.5 53.9 1.0 N B:THR199 4.5 54.4 1.0 OG1 B:THR199 4.6 48.9 1.0 N B:TYR200 4.7 50.8 1.0 N B:PRO198 4.8 60.8 1.0 O B:CYS197 4.8 53.5 1.0 ND2 B:ASN118 4.9 41.0 1.0 SG B:CYS15 4.9 51.1 1.0 CA B:THR199 4.9 53.4 1.0

Iron binding site 4 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:39.5 occ:0.70 FE4 B:SF4401 0.0 39.5 0.7 S1 B:SF4401 2.2 38.9 0.7 S3 B:SF4401 2.2 41.6 0.7 S2 B:SF4401 2.2 45.1 0.7 SG B:CYS15 2.3 51.1 1.0 FE1 B:SF4401 2.8 38.9 0.7 FE2 B:SF4401 2.8 35.8 0.7 FE3 B:SF4401 2.9 37.3 0.7 CB B:CYS15 3.1 50.0 1.0 S4 B:SF4401 3.7 40.8 0.7 CA B:CYS15 4.2 48.8 1.0 OD2 B:ASP17 4.3 48.0 1.0 CB B:CYS46 4.6 47.3 1.0 N B:CYS12 4.7 49.8 1.0 CB B:CYS12 4.7 48.1 1.0 CA B:CYS197 4.7 52.2 1.0 SG B:CYS197 4.8 44.3 1.0 SG B:CYS46 4.8 44.2 1.0 SG B:CYS12 4.9 45.4 1.0 CB B:CYS197 4.9 50.1 1.0 CB B:TRP11 4.9 52.0 1.0 CD1 B:TRP11 4.9 53.1 1.0 CG B:ASP17 4.9 53.1 1.0

Z.Yan, A.Maruyama, T.Arakawa, S.Fushinobu, T.Wakagi. Crystal Structures of Archaeal 2-Oxoacid:Ferredoxin Oxidoreductases From Sulfolobus Tokodaii Sci Rep V. 6 33061 2016.
ISSN: ESSN 2045-2322
PubMed: 27619895
DOI: 10.1038/SREP33061