Iron in PDB 9i2a: Fdc of Rhodobacter Capsulatus

The structure of Fdc of Rhodobacter Capsulatus, PDB code: 9i2a was solved by P.Pfister, H.G.Addison, T.J.Erb, J.G.Rebelein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.34 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.87, 45.83, 85.3, 90, 90, 90
R / Rfree (%)	17.7 / 18.4

The binding sites of Iron atom in the Fdc of Rhodobacter Capsulatus (pdb code 9i2a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Fdc of Rhodobacter Capsulatus, PDB code: 9i2a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Fdc of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fdc of Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:20.4 occ:1.00 FE1 A:FES101 0.0 20.4 1.0 S1 A:FES101 2.2 21.1 1.0 S2 A:FES101 2.2 19.9 1.0 SG A:CYS43 2.3 20.0 1.0 SG A:CYS38 2.3 21.6 1.0 FE2 A:FES101 2.7 19.6 1.0 CB A:CYS38 3.4 21.3 1.0 CB A:CYS43 3.5 21.0 1.0 N A:CYS43 3.5 22.0 1.0 N A:GLY44 3.6 21.0 1.0 N A:CYS38 3.8 21.6 1.0 CA A:CYS43 4.0 21.4 1.0 CA A:CYS38 4.0 20.8 1.0 O A:HOH247 4.1 21.2 1.0 N A:GLU42 4.2 23.2 1.0 O A:CYS38 4.2 20.7 1.0 C A:CYS43 4.3 21.5 1.0 CA A:GLY41 4.3 23.9 1.0 C A:CYS38 4.3 21.0 1.0 C A:GLY37 4.4 21.8 1.0 SG A:CYS81 4.4 18.4 1.0 N A:GLY41 4.5 23.0 1.0 C A:GLY41 4.5 21.9 1.0 N A:GLY37 4.5 19.2 1.0 OG1 A:THR45 4.5 21.1 1.0 N A:THR45 4.5 19.8 1.0 SG A:CYS46 4.6 18.1 1.0 CA A:GLY44 4.6 20.9 1.0 C A:GLU42 4.6 22.6 1.0 CA A:GLY37 4.8 20.2 1.0 CA A:GLU42 5.0 23.1 1.0

Iron binding site 2 out of 4 in the Fdc of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fdc of Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:19.6 occ:1.00 FE2 A:FES101 0.0 19.6 1.0 S2 A:FES101 2.2 19.9 1.0 S1 A:FES101 2.2 21.1 1.0 SG A:CYS81 2.3 18.4 1.0 SG A:CYS46 2.3 18.1 1.0 FE1 A:FES101 2.7 20.4 1.0 CB A:CYS81 3.3 18.0 1.0 CB A:CYS46 3.5 18.2 1.0 O A:HOH247 3.9 21.2 1.0 N A:CYS81 4.2 18.4 1.0 CA A:CYS81 4.4 18.1 1.0 N A:CYS46 4.4 18.2 1.0 SG A:CYS43 4.5 20.0 1.0 SG A:CYS38 4.5 21.6 1.0 CA A:CYS46 4.5 18.4 1.0 CA A:GLY41 4.6 23.9 1.0 CB A:LEU79 4.6 18.6 1.0 OE1 A:GLN82 4.7 21.4 1.0 N A:GLY44 4.7 21.0 1.0 CD1 A:LEU79 4.9 19.6 1.0 CA A:GLY44 5.0 20.9 1.0

Iron binding site 3 out of 4 in the Fdc of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fdc of Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:23.9 occ:1.00 FE1 B:FES101 0.0 23.9 1.0 S2 B:FES101 2.2 24.6 1.0 S1 B:FES101 2.2 22.0 1.0 SG B:CYS43 2.2 24.4 1.0 SG B:CYS38 2.4 26.5 1.0 FE2 B:FES101 2.7 23.1 1.0 N B:CYS38 3.3 26.4 1.0 CB B:CYS38 3.5 25.2 1.0 CB B:CYS43 3.5 23.3 1.0 N B:GLY44 3.6 24.0 1.0 N B:CYS43 3.6 25.4 1.0 CA B:CYS38 3.9 25.3 1.0 CA B:CYS43 4.0 23.7 1.0 O B:CYS38 4.1 25.8 1.0 C B:GLY37 4.1 24.8 1.0 C B:CYS43 4.2 23.8 1.0 N B:GLU42 4.2 25.3 1.0 CA B:GLY37 4.3 22.8 1.0 C B:CYS38 4.3 26.1 1.0 CA B:GLY41 4.3 25.5 1.0 O B:HOH220 4.3 25.1 1.0 N B:GLY37 4.4 20.9 1.0 SG B:CYS81 4.4 18.8 1.0 N B:GLY41 4.5 26.6 1.0 C B:GLY41 4.5 24.7 1.0 N B:THR45 4.5 22.0 1.0 SG B:CYS46 4.6 18.6 1.0 CA B:GLY44 4.6 23.3 1.0 C B:GLU42 4.7 25.1 1.0 OG1 B:THR45 4.8 21.5 1.0 C B:GLY44 5.0 22.3 1.0

Iron binding site 4 out of 4 in the Fdc of Rhodobacter Capsulatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fdc of Rhodobacter Capsulatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:23.1 occ:1.00 FE2 B:FES101 0.0 23.1 1.0 S1 B:FES101 2.2 22.0 1.0 S2 B:FES101 2.2 24.6 1.0 SG B:CYS81 2.3 18.8 1.0 SG B:CYS46 2.3 18.6 1.0 FE1 B:FES101 2.7 23.9 1.0 CB B:CYS81 3.3 19.2 1.0 CB B:CYS46 3.4 20.2 1.0 O B:HOH220 4.1 25.1 1.0 N B:CYS81 4.2 18.7 1.0 CA B:CYS81 4.4 19.3 1.0 N B:CYS46 4.4 20.0 1.0 CA B:GLY41 4.5 25.5 1.0 SG B:CYS38 4.5 26.5 1.0 CA B:CYS46 4.5 19.5 1.0 SG B:CYS43 4.6 24.4 1.0 CB B:LEU79 4.7 19.5 1.0 N B:GLY44 4.7 24.0 1.0 NE2 B:GLN82 4.9 21.6 1.0 CA B:GLY44 5.0 23.3 1.0 C B:GLY41 5.0 24.7 1.0

H.Addison, P.Pfister, A.Lago-Maciel, T.J.Erb, A.J.Pierik, J.G.Rebelein. Two Key Ferredoxins For Nitrogen Fixation Have Different Specificities and Biophysical Properties. Chemistry 00844 2025.
ISSN: ISSN 0947-6539
PubMed: 40396536
DOI: 10.1002/CHEM.202500844