Iron in PDB 1fdn: Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution

The structure of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution, PDB code: 1fdn was solved by E.Duee, E.Fanchon, J.Vicat, L.C.Sieker, J.Meyer, J-M.Moulis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 1.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	34.440, 34.440, 74.780, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / n/a

The binding sites of Iron atom in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution (pdb code 1fdn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution, PDB code: 1fdn:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe56 b:10.8 occ:1.00 FE1 A:SF456 0.0 10.8 1.0 SG A:CYS47 2.2 9.2 1.0 S4 A:SF456 2.3 9.5 1.0 S3 A:SF456 2.3 9.7 1.0 S2 A:SF456 2.3 10.9 1.0 FE2 A:SF456 2.7 10.5 1.0 FE4 A:SF456 2.7 11.0 1.0 FE3 A:SF456 2.7 10.2 1.0 CB A:CYS47 3.3 10.0 1.0 CA A:CYS47 3.8 9.8 1.0 S1 A:SF456 3.8 10.5 1.0 CD A:PRO48 4.3 9.2 1.0 CG2 A:VAL49 4.4 11.0 1.0 CB A:ALA51 4.4 8.8 1.0 CD A:PRO52 4.5 9.3 1.0 SG A:CYS11 4.6 10.7 1.0 C A:CYS47 4.6 8.7 1.0 SG A:CYS14 4.7 10.6 1.0 N A:PRO48 4.8 9.4 1.0 N A:ALA51 4.8 10.6 1.0 SG A:CYS8 4.8 8.2 1.0 CG A:PRO52 4.9 9.8 1.0 N A:CYS47 4.9 9.4 1.0

Iron binding site 2 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe56 b:10.5 occ:1.00 FE2 A:SF456 0.0 10.5 1.0 SG A:CYS14 2.2 10.6 1.0 S3 A:SF456 2.3 9.7 1.0 S4 A:SF456 2.3 9.5 1.0 S1 A:SF456 2.3 10.5 1.0 FE3 A:SF456 2.7 10.2 1.0 FE1 A:SF456 2.7 10.8 1.0 FE4 A:SF456 2.8 11.0 1.0 CB A:CYS14 3.3 10.2 1.0 S2 A:SF456 3.8 10.9 1.0 N A:CYS14 3.9 11.1 1.0 CA A:CYS14 4.2 11.6 1.0 SG A:CYS8 4.7 8.2 1.0 CB A:TYR30 4.7 11.4 1.0 SG A:CYS11 4.7 10.7 1.0 SG A:CYS47 4.8 9.2 1.0 CG A:TYR30 4.8 11.9 1.0 N A:ALA13 4.8 11.5 1.0 CD1 A:ILE4 4.9 10.3 1.0 N A:GLY12 4.9 10.8 1.0

Iron binding site 3 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe56 b:10.2 occ:1.00 FE3 A:SF456 0.0 10.2 1.0 SG A:CYS8 2.2 8.2 1.0 S2 A:SF456 2.2 10.9 1.0 S4 A:SF456 2.3 9.5 1.0 S1 A:SF456 2.3 10.5 1.0 FE2 A:SF456 2.7 10.5 1.0 FE1 A:SF456 2.7 10.8 1.0 FE4 A:SF456 2.8 11.0 1.0 CB A:CYS8 3.3 9.1 1.0 CA A:CYS8 3.8 10.1 1.0 S3 A:SF456 3.9 9.7 1.0 N A:SER10 3.9 11.9 1.0 N A:ILE9 4.1 10.9 1.0 C A:CYS8 4.3 10.9 1.0 CA A:SER10 4.4 11.9 1.0 CG2 A:ILE4 4.5 7.8 1.0 CB A:TYR30 4.5 11.4 1.0 N A:CYS11 4.6 11.7 1.0 CD1 A:TYR30 4.6 11.1 1.0 SG A:CYS47 4.7 9.2 1.0 SG A:CYS14 4.7 10.6 1.0 CG A:TYR30 4.8 11.9 1.0 CB A:ALA51 4.9 8.8 1.0 C A:ILE9 4.9 11.9 1.0

Iron binding site 4 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe56 b:11.0 occ:1.00 FE4 A:SF456 0.0 11.0 1.0 S3 A:SF456 2.2 9.7 1.0 S1 A:SF456 2.2 10.5 1.0 S2 A:SF456 2.3 10.9 1.0 SG A:CYS11 2.3 10.7 1.0 FE1 A:SF456 2.7 10.8 1.0 FE2 A:SF456 2.8 10.5 1.0 FE3 A:SF456 2.8 10.2 1.0 CB A:CYS11 3.4 11.6 1.0 N A:CYS11 3.5 11.7 1.0 N A:GLY12 3.7 10.8 1.0 CA A:CYS11 3.9 11.6 1.0 S4 A:SF456 3.9 9.5 1.0 C A:CYS11 4.1 12.3 1.0 N A:ALA13 4.2 11.5 1.0 CD A:PRO48 4.5 9.2 1.0 C A:SER10 4.6 12.1 1.0 N A:SER10 4.6 11.9 1.0 CA A:GLY12 4.6 11.1 1.0 SG A:CYS47 4.6 9.2 1.0 SG A:CYS14 4.7 10.6 1.0 SG A:CYS8 4.8 8.2 1.0 CA A:SER10 4.8 11.9 1.0 C A:GLY12 4.8 10.8 1.0 CG1 A:ILE9 4.8 11.4 1.0 CB A:ALA13 4.8 13.3 1.0 N A:CYS14 4.9 11.1 1.0 CG A:PRO48 4.9 10.4 1.0

Iron binding site 5 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe57 b:10.8 occ:1.00 FE1 A:SF457 0.0 10.8 1.0 S4 A:SF457 2.3 9.4 1.0 S3 A:SF457 2.3 9.8 1.0 SG A:CYS18 2.3 9.7 1.0 S2 A:SF457 2.3 10.0 1.0 FE4 A:SF457 2.7 10.6 1.0 FE3 A:SF457 2.7 10.5 1.0 FE2 A:SF457 2.7 10.2 1.0 CB A:CYS18 3.3 11.2 1.0 S1 A:SF457 3.8 9.7 1.0 CA A:CYS18 3.9 11.5 1.0 CB A:ALA22 4.2 10.5 1.0 CD A:PRO19 4.3 12.2 1.0 CG2 A:VAL20 4.5 9.6 1.0 SG A:CYS40 4.6 10.6 1.0 C A:CYS18 4.6 11.0 1.0 CD1 A:ILE23 4.6 10.7 1.0 CG1 A:ILE23 4.6 11.7 1.0 N A:PRO19 4.7 11.7 1.0 SG A:CYS43 4.8 9.6 1.0 N A:ALA22 4.8 11.6 1.0 SG A:CYS37 4.9 9.2 1.0

Iron binding site 6 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe57 b:10.2 occ:1.00 FE2 A:SF457 0.0 10.2 1.0 SG A:CYS43 2.2 9.6 1.0 S3 A:SF457 2.3 9.8 1.0 S4 A:SF457 2.3 9.4 1.0 S1 A:SF457 2.3 9.7 1.0 FE3 A:SF457 2.7 10.5 1.0 FE1 A:SF457 2.7 10.8 1.0 FE4 A:SF457 2.8 10.6 1.0 CB A:CYS43 3.3 9.8 1.0 S2 A:SF457 3.9 10.0 1.0 N A:CYS43 3.9 9.8 1.0 CA A:CYS43 4.2 10.3 1.0 CD1 A:ILE23 4.4 10.7 1.0 CD1 A:ILE32 4.6 9.9 1.0 SG A:CYS40 4.7 10.6 1.0 SG A:CYS37 4.7 9.2 1.0 N A:ALA42 4.7 10.9 1.0 CB A:TYR2 4.8 11.1 1.0 SG A:CYS18 4.8 9.7 1.0 CG A:TYR2 4.8 11.9 1.0 N A:GLY41 4.9 10.6 1.0 CG1 A:ILE23 5.0 11.7 1.0 CD2 A:TYR2 5.0 11.5 1.0

Iron binding site 7 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe57 b:10.5 occ:1.00 FE3 A:SF457 0.0 10.5 1.0 S2 A:SF457 2.2 10.0 1.0 SG A:CYS37 2.3 9.2 1.0 S4 A:SF457 2.3 9.4 1.0 S1 A:SF457 2.3 9.7 1.0 FE2 A:SF457 2.7 10.2 1.0 FE1 A:SF457 2.7 10.8 1.0 FE4 A:SF457 2.8 10.6 1.0 CB A:CYS37 3.3 9.8 1.0 CA A:CYS37 3.7 10.4 1.0 S3 A:SF457 3.8 9.8 1.0 N A:ILE38 4.0 11.4 1.0 N A:ASP39 4.1 12.7 1.0 C A:CYS37 4.3 10.7 1.0 CB A:TYR2 4.7 11.1 1.0 CA A:ASP39 4.7 12.5 1.0 N A:CYS40 4.7 11.6 1.0 CG2 A:ILE32 4.7 8.5 1.0 SG A:CYS43 4.8 9.6 1.0 SG A:CYS18 4.8 9.7 1.0 CD1 A:TYR2 4.9 11.4 1.0 CB A:ALA22 4.9 10.5 1.0 N A:TYR2 4.9 11.2 1.0 CG A:TYR2 5.0 11.9 1.0 N A:CYS37 5.0 11.0 1.0 C A:ILE38 5.0 12.4 1.0

Iron binding site 8 out of 8 in the Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe57 b:10.6 occ:1.00 FE4 A:SF457 0.0 10.6 1.0 S3 A:SF457 2.2 9.8 1.0 S1 A:SF457 2.3 9.7 1.0 S2 A:SF457 2.3 10.0 1.0 SG A:CYS40 2.3 10.6 1.0 FE1 A:SF457 2.7 10.8 1.0 FE2 A:SF457 2.8 10.2 1.0 FE3 A:SF457 2.8 10.5 1.0 CB A:CYS40 3.4 10.7 1.0 N A:CYS40 3.6 11.6 1.0 N A:GLY41 3.8 10.6 1.0 S4 A:SF457 3.9 9.4 1.0 CA A:CYS40 3.9 11.5 1.0 N A:ALA42 4.1 10.9 1.0 C A:CYS40 4.2 12.0 1.0 CD A:PRO19 4.3 12.2 1.0 CD1 A:ILE38 4.4 13.5 1.0 CB A:ALA42 4.6 10.8 1.0 C A:ASP39 4.6 12.8 1.0 SG A:CYS18 4.6 9.7 1.0 SG A:CYS43 4.7 9.6 1.0 CG A:PRO19 4.7 12.8 1.0 CA A:GLY41 4.7 10.6 1.0 SG A:CYS37 4.8 9.2 1.0 N A:ASP39 4.8 12.7 1.0 C A:GLY41 4.8 11.1 1.0 N A:CYS43 4.9 9.8 1.0 CA A:ALA42 4.9 11.2 1.0 CA A:ASP39 5.0 12.5 1.0

E.D.Duee, E.Fanchon, J.Vicat, L.C.Sieker, J.Meyer, J.M.Moulis. Refined Crystal Structure of the 2[4FE-4S] Ferredoxin From Clostridium Acidurici at 1.84 A Resolution. J.Mol.Biol. V. 243 683 1994.
ISSN: ISSN 0022-2836
PubMed: 7966291
DOI: 10.1016/0022-2836(94)90041-8