Iron in PDB 1ir0: Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II)

The structure of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II), PDB code: 1ir0 was solved by K.Fukuyama, T.Okada, Y.Kakuta, Y.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.30 / 1.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.560, 30.380, 50.920, 90.00, 124.02, 90.00
R / Rfree (%)	9.6 / 12

The binding sites of Iron atom in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II) (pdb code 1ir0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II), PDB code: 1ir0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe82 b:3.1 occ:1.00 FE1 A:SF482 0.0 3.1 1.0 S2 A:SF482 2.3 3.3 1.0 SG A:CYS61 2.3 4.0 1.0 S4 A:SF482 2.3 3.4 1.0 S3 A:SF482 2.3 3.8 1.0 FE4 A:SF482 2.7 3.1 1.0 FE3 A:SF482 2.7 2.9 1.0 FE2 A:SF482 2.8 3.3 1.0 CB A:CYS61 3.3 3.8 1.0 CA A:CYS61 3.9 3.6 1.0 S1 A:SF482 3.9 3.5 1.0 OG1 A:THR63 4.1 8.0 1.0 CD A:PRO62 4.2 4.4 1.0 CB A:SER65 4.2 3.8 1.0 CG1 A:ILE66 4.4 4.8 1.0 CD1 A:ILE66 4.5 6.1 1.0 C A:CYS61 4.5 3.4 1.0 OG A:SER65 4.6 5.7 1.0 N A:PRO62 4.6 3.7 1.0 SG A:CYS14 4.7 4.1 1.0 N A:ILE66 4.8 2.9 1.0 N A:SER65 4.8 3.5 1.0 SG A:CYS17 4.8 3.7 1.0 SG A:CYS11 4.9 3.6 1.0 CA A:SER65 5.0 3.2 1.0

Iron binding site 2 out of 4 in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe82 b:3.3 occ:1.00 FE2 A:SF482 0.0 3.3 1.0 SG A:CYS14 2.3 4.1 1.0 S1 A:SF482 2.3 3.5 1.0 S3 A:SF482 2.3 3.8 1.0 S4 A:SF482 2.3 3.4 1.0 FE4 A:SF482 2.8 3.1 1.0 FE1 A:SF482 2.8 3.1 1.0 FE3 A:SF482 2.8 2.9 1.0 CB A:CYS14 3.5 4.5 1.0 N A:CYS14 3.6 4.6 1.0 S2 A:SF482 3.9 3.3 1.0 CA A:CYS14 4.0 4.8 1.0 CD A:PRO62 4.1 4.4 1.0 N A:ALA16 4.3 4.7 1.0 N A:GLY15 4.3 5.5 1.0 C A:CYS14 4.4 4.2 1.0 N A:ALA13 4.5 3.9 1.0 CB A:ALA16 4.6 5.1 1.0 CG A:PRO62 4.6 5.0 1.0 C A:ALA13 4.7 4.0 1.0 SG A:CYS61 4.7 4.0 1.0 SG A:CYS17 4.8 3.7 1.0 SG A:CYS11 4.8 3.6 1.0 CA A:ALA13 4.8 3.6 1.0 N A:CYS17 4.9 4.3 1.0 CG1 A:ILE12 4.9 6.1 1.0 CA A:ALA16 5.0 4.6 1.0

Iron binding site 3 out of 4 in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe82 b:2.9 occ:1.00 FE3 A:SF482 0.0 2.9 1.0 S4 A:SF482 2.2 3.4 1.0 SG A:CYS17 2.3 3.7 1.0 S2 A:SF482 2.3 3.3 1.0 S1 A:SF482 2.3 3.5 1.0 FE4 A:SF482 2.7 3.1 1.0 FE1 A:SF482 2.7 3.1 1.0 FE2 A:SF482 2.8 3.3 1.0 CB A:CYS17 3.2 3.6 1.0 CB A:ALA33 3.8 4.3 1.0 N A:CYS17 3.9 4.3 1.0 S3 A:SF482 3.9 3.8 1.0 CA A:CYS17 4.2 4.2 1.0 CD1 A:ILE66 4.2 6.1 1.0 SG A:CYS11 4.6 3.6 1.0 CG1 A:ILE66 4.7 4.8 1.0 SG A:CYS14 4.7 4.1 1.0 SG A:CYS61 4.8 4.0 1.0 N A:ALA16 4.9 4.7 1.0

Iron binding site 4 out of 4 in the Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe82 b:3.1 occ:1.00 FE4 A:SF482 0.0 3.1 1.0 S3 A:SF482 2.3 3.8 1.0 SG A:CYS11 2.3 3.6 1.0 S2 A:SF482 2.3 3.3 1.0 S1 A:SF482 2.3 3.5 1.0 FE3 A:SF482 2.7 2.9 1.0 FE1 A:SF482 2.7 3.1 1.0 FE2 A:SF482 2.8 3.3 1.0 CB A:CYS11 3.3 3.8 1.0 CA A:CYS11 3.8 4.0 1.0 S4 A:SF482 3.9 3.4 1.0 N A:ALA13 3.9 3.9 1.0 CB A:ALA33 3.9 4.3 1.0 N A:ILE12 4.0 3.8 1.0 C A:CYS11 4.3 4.4 1.0 CA A:ALA13 4.5 3.6 1.0 SG A:CYS17 4.7 3.7 1.0 N A:CYS14 4.7 4.6 1.0 CB A:SER65 4.8 3.8 1.0 SG A:CYS61 4.8 4.0 1.0 C A:ILE12 4.8 4.5 1.0 OG A:SER65 4.9 5.7 1.0 N A:ALA33 4.9 3.3 1.0 SG A:CYS14 4.9 4.1 1.0 CG1 A:VAL6 5.0 3.5 1.0 CA A:ILE12 5.0 4.9 1.0

K.Fukuyama, T.Okada, Y.Kakuta, Y.Takahashi. Atomic Resolution Structures of Oxidized [4FE-4S] Ferredoxin From Bacillus Thermoproteolyticus in Two Crystal Forms: Systematic Distortion of [4FE-4S] Cluster in the Protein. J.Mol.Biol. V. 315 1155 2002.
ISSN: ISSN 0022-2836
PubMed: 11827483
DOI: 10.1006/JMBI.2001.5292