Iron in PDB 5b48: 2-Oxoacid:Ferredoxin Oxidoreductase 1 From Sulfolobus Tokodai

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 1 From Sulfolobus Tokodai, PDB code: 5b48 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)	36.47 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.150, 145.878, 170.094, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 27.8

The structure of 2-Oxoacid:Ferredoxin Oxidoreductase 1 From Sulfolobus Tokodai also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the 2-Oxoacid:Ferredoxin Oxidoreductase 1 From Sulfolobus Tokodai (pdb code 5b48). 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 1 From Sulfolobus Tokodai, PDB code: 5b48:
Jump to Iron binding site number: 1; 2; 3; 4;

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


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 1 From Sulfolobus Tokodai within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:63.6 occ:1.00 FE1 B:SF4401 0.0 63.6 1.0 S3 B:SF4401 2.1 58.4 1.0 S4 B:SF4401 2.1 58.5 1.0 S2 B:SF4401 2.2 55.7 1.0 SG B:CYS197 2.2 63.7 1.0 FE3 B:SF4401 3.1 65.5 1.0 FE4 B:SF4401 3.1 66.1 1.0 CB B:CYS197 3.2 70.2 1.0 FE2 B:SF4401 3.2 64.4 1.0 CA B:CYS197 3.6 72.6 1.0 S1 B:SF4401 3.8 56.7 1.0 C B:CYS197 4.2 67.2 1.0 CB B:THR199 4.4 70.8 1.0 N B:THR199 4.6 69.8 1.0 OG1 B:THR199 4.6 66.9 1.0 OD1 B:ASN118 4.6 90.7 1.0 CD2 B:TYR200 4.6 60.2 1.0 O B:CYS197 4.7 70.8 1.0 N B:TYR200 4.7 62.5 1.0 N B:PRO198 4.8 69.6 1.0 ND2 B:ASN118 4.8 63.0 1.0 N B:CYS197 4.9 70.6 1.0 CA B:THR199 4.9 67.0 1.0 CA B:GLY122 5.0 66.2 1.0

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


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 1 From Sulfolobus Tokodai within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:64.4 occ:1.00 FE2 B:SF4401 0.0 64.4 1.0 S4 B:SF4401 2.1 58.5 1.0 S1 B:SF4401 2.2 56.7 1.0 S3 B:SF4401 2.2 58.4 1.0 SG B:CYS12 2.3 69.0 1.0 FE3 B:SF4401 3.1 65.5 1.0 CB B:CYS12 3.1 67.6 1.0 FE4 B:SF4401 3.1 66.1 1.0 FE1 B:SF4401 3.2 63.6 1.0 OG1 B:THR199 3.4 66.9 1.0 S2 B:SF4401 3.7 55.7 1.0 N B:CYS12 3.8 58.6 1.0 CB B:THR199 4.0 70.8 1.0 CA B:CYS12 4.1 69.6 1.0 CB A:ILE43 4.4 54.4 1.0 CG2 A:ILE43 4.4 54.9 1.0 CG2 B:THR199 4.8 66.2 1.0 CG1 A:ILE43 4.9 59.1 1.0

Iron binding site 3 out of 4 in the 2-Oxoacid:Ferredoxin Oxidoreductase 1 From Sulfolobus Tokodai


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 1 From Sulfolobus Tokodai within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:65.5 occ:1.00 FE3 B:SF4401 0.0 65.5 1.0 S2 B:SF4401 2.1 55.7 1.0 S4 B:SF4401 2.1 58.5 1.0 S1 B:SF4401 2.2 56.7 1.0 SG B:CYS46 2.3 61.3 1.0 FE2 B:SF4401 3.1 64.4 1.0 FE4 B:SF4401 3.1 66.1 1.0 FE1 B:SF4401 3.1 63.6 1.0 CB B:CYS46 3.1 60.1 1.0 S3 B:SF4401 3.6 58.4 1.0 CA B:GLY122 4.3 66.2 1.0 C B:GLY122 4.4 63.2 1.0 CA B:CYS46 4.6 63.4 1.0 N B:LEU123 4.6 68.4 1.0 O B:GLY122 4.8 62.3 1.0 CG1 A:ILE43 4.8 59.1 1.0 SG B:CYS197 5.0 63.7 1.0

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


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 1 From Sulfolobus Tokodai within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:66.1 occ:1.00 FE4 B:SF4401 0.0 66.1 1.0 S3 B:SF4401 2.1 58.4 1.0 S2 B:SF4401 2.2 55.7 1.0 S1 B:SF4401 2.2 56.7 1.0 SG B:CYS15 2.2 73.1 1.0 FE3 B:SF4401 3.1 65.5 1.0 FE2 B:SF4401 3.1 64.4 1.0 FE1 B:SF4401 3.1 63.6 1.0 CB B:CYS15 3.2 81.8 1.0 S4 B:SF4401 3.7 58.5 1.0 CA B:CYS15 4.2 80.3 1.0 ND2 B:ASN17 4.5 53.6 1.0 OE1 B:GLN195 4.6 63.6 1.0 N B:CYS12 4.6 58.6 1.0 O B:GLY14 4.8 0.2 1.0 CB B:CYS12 4.8 67.6 1.0 CB B:CYS46 4.8 60.1 1.0 CB B:TRP11 5.0 64.4 1.0 C B:CYS15 5.0 71.3 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