Iron in PDB 5b47: 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex, PDB code: 5b47 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)	36.17 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.673, 203.655, 126.006, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.9

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex 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 - Pyruvate Complex (pdb code 5b47). 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 - Pyruvate Complex, PDB code: 5b47:
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 - Pyruvate Complex


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 - Pyruvate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:64.5 occ:0.70 FE1 B:SF4401 0.0 64.5 0.7 S2 B:SF4401 2.1 77.0 0.7 S3 B:SF4401 2.2 65.1 0.7 S4 B:SF4401 2.2 65.0 0.7 SG B:CYS15 2.5 85.9 1.0 FE2 B:SF4401 3.1 71.9 0.7 FE3 B:SF4401 3.1 70.3 0.7 FE4 B:SF4401 3.1 62.4 0.7 CB B:CYS15 3.5 0.0 1.0 S1 B:SF4401 3.8 72.2 0.7 CA B:CYS15 4.0 0.3 1.0 OD2 B:ASP17 4.4 80.3 1.0 N B:CYS12 4.7 81.8 1.0 CB B:TRP11 4.7 0.6 1.0 C B:CYS15 4.7 0.5 1.0 O B:CYS15 4.8 0.8 1.0 CB B:CYS46 4.8 95.6 1.0 CB B:CYS12 4.8 79.4 1.0 CD1 B:TRP11 4.9 1.0 1.0 CG B:TRP11 4.9 0.4 1.0

Iron binding site 2 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex


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 - Pyruvate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:71.9 occ:0.70 FE2 B:SF4401 0.0 71.9 0.7 S4 B:SF4401 2.1 65.0 0.7 S1 B:SF4401 2.2 72.2 0.7 S3 B:SF4401 2.2 65.1 0.7 SG B:CYS46 2.3 75.7 1.0 CB B:CYS46 3.0 95.6 1.0 FE3 B:SF4401 3.1 70.3 0.7 FE4 B:SF4401 3.1 62.4 0.7 FE1 B:SF4401 3.1 64.5 0.7 S2 B:SF4401 3.7 77.0 0.7 CA B:GLY122 4.3 86.0 1.0 CG1 A:ILE44 4.3 71.1 1.0 C B:GLY122 4.4 83.9 1.0 N B:LEU123 4.5 85.9 1.0 CA B:CYS46 4.5 0.4 1.0 O1B B:TPP402 4.8 87.6 1.0 CB A:ILE44 4.9 69.2 1.0 O B:GLY122 5.0 75.2 1.0

Iron binding site 3 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex


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 - Pyruvate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:70.3 occ:0.70 FE3 B:SF4401 0.0 70.3 0.7 S2 B:SF4401 2.1 77.0 0.7 S1 B:SF4401 2.2 72.2 0.7 S4 B:SF4401 2.2 65.0 0.7 SG B:CYS12 2.4 82.0 1.0 FE2 B:SF4401 3.1 71.9 0.7 FE4 B:SF4401 3.1 62.4 0.7 FE1 B:SF4401 3.1 64.5 0.7 CB B:CYS12 3.2 79.4 1.0 S3 B:SF4401 3.7 65.1 0.7 N B:CYS12 3.8 81.8 1.0 OG1 B:THR199 3.9 72.5 1.0 CB A:ILE44 4.0 69.2 1.0 CG2 A:ILE44 4.1 69.0 1.0 CA B:CYS12 4.2 90.7 1.0 CB B:THR199 4.3 90.1 1.0 CG1 A:ILE44 4.5 71.1 1.0 C B:TRP11 5.0 86.0 1.0

Iron binding site 4 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 2 From Sulfolobus Tokodai - Pyruvate Complex


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 - Pyruvate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:62.4 occ:0.70 FE4 B:SF4401 0.0 62.4 0.7 S1 B:SF4401 2.1 72.2 0.7 S3 B:SF4401 2.2 65.1 0.7 S2 B:SF4401 2.2 77.0 0.7 SG B:CYS197 2.4 88.8 1.0 FE3 B:SF4401 3.1 70.3 0.7 FE2 B:SF4401 3.1 71.9 0.7 FE1 B:SF4401 3.1 64.5 0.7 CB B:CYS197 3.5 97.5 1.0 S4 B:SF4401 3.7 65.0 0.7 CA B:CYS197 4.2 93.4 1.0 C B:CYS197 4.4 91.8 1.0 ND2 B:ASN118 4.4 81.9 1.0 CD2 B:TYR200 4.4 98.2 1.0 CA B:GLY122 4.5 86.0 1.0 N B:TYR200 4.5 0.2 1.0 CB B:THR199 4.6 90.1 1.0 N B:THR199 4.6 97.3 1.0 O B:CYS197 4.7 69.7 1.0 N B:PRO198 4.9 0.2 1.0 OG1 B:THR199 4.9 72.5 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