Iron in PDB 3exy: Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum

The structure of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum, PDB code: 3exy was solved by P.Giastas, E.Saridakis, I.M.Mavridis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.48
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.425, 51.425, 76.425, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 21.8

The binding sites of Iron atom in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum (pdb code 3exy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum, PDB code: 3exy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe83 b:16.2 occ:1.00 FE1 A:SF483 0.0 16.2 1.0 S2 A:SF483 2.3 15.7 1.0 S3 A:SF483 2.3 16.4 1.0 S4 A:SF483 2.3 15.7 1.0 SG A:CYS8 2.3 17.0 1.0 FE3 A:SF483 2.7 15.4 1.0 FE2 A:SF483 2.7 16.2 1.0 FE4 A:SF483 2.7 15.7 1.0 CB A:CYS8 3.2 18.4 1.0 CA A:CYS8 3.7 18.1 1.0 S1 A:SF483 3.8 15.3 1.0 N A:ILE9 4.0 17.1 1.0 N A:ASN10 4.0 16.7 1.0 SG A:CYS57 4.1 17.5 1.0 C A:CYS8 4.2 18.1 1.0 N A:CYS11 4.5 17.4 1.0 CA A:ASN10 4.5 16.2 1.0 CG2 A:ILE4 4.6 14.9 1.0 CB A:TYR30 4.6 17.1 1.0 CD1 A:TYR30 4.7 23.2 1.0 SG A:CYS14 4.7 16.3 1.0 SG A:CYS53 4.8 15.7 1.0 SG A:CYS11 4.9 17.2 1.0 C A:ILE9 4.9 15.9 1.0 CG A:TYR30 5.0 19.9 1.0

Iron binding site 2 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe83 b:16.2 occ:1.00 FE2 A:SF483 0.0 16.2 1.0 S4 A:SF483 2.3 15.7 1.0 SG A:CYS11 2.3 17.2 1.0 S3 A:SF483 2.3 16.4 1.0 S1 A:SF483 2.3 15.3 1.0 FE3 A:SF483 2.7 15.4 1.0 FE1 A:SF483 2.7 16.2 1.0 FE4 A:SF483 2.7 15.7 1.0 CB A:CYS11 3.4 18.8 1.0 N A:CYS11 3.5 17.4 1.0 S2 A:SF483 3.9 15.7 1.0 CA A:CYS11 3.9 18.3 1.0 CD A:PRO54 3.9 19.1 1.0 N A:ASP12 4.1 17.2 1.0 N A:GLY13 4.2 17.6 1.0 C A:CYS11 4.3 20.9 1.0 CG A:PRO54 4.4 22.1 1.0 SG A:CYS14 4.7 16.3 1.0 C A:ASN10 4.7 17.1 1.0 SG A:CYS53 4.7 15.7 1.0 SG A:CYS8 4.7 17.0 1.0 N A:ASN10 4.7 16.7 1.0 N A:CYS14 4.8 17.1 1.0 CG1 A:ILE9 4.8 17.8 1.0 CA A:GLY13 4.9 18.2 1.0 CA A:ASN10 5.0 16.2 1.0

Iron binding site 3 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe83 b:15.4 occ:1.00 FE3 A:SF483 0.0 15.4 1.0 S1 A:SF483 2.2 15.3 1.0 SG A:CYS14 2.3 16.3 1.0 S4 A:SF483 2.3 15.7 1.0 S2 A:SF483 2.3 15.7 1.0 FE1 A:SF483 2.7 16.2 1.0 FE2 A:SF483 2.7 16.2 1.0 FE4 A:SF483 2.7 15.7 1.0 CB A:CYS14 3.3 16.9 1.0 S3 A:SF483 3.9 16.4 1.0 N A:CYS14 3.9 17.1 1.0 CA A:CYS14 4.2 16.1 1.0 O A:HOH114 4.3 30.3 1.0 CD1 A:ILE58 4.5 15.7 1.0 CB A:TYR30 4.6 17.1 1.0 CD1 A:ILE4 4.6 15.6 1.0 SG A:CYS11 4.6 17.2 1.0 SG A:CYS8 4.6 17.0 1.0 CG A:TYR30 4.8 19.9 1.0 N A:GLY13 4.8 17.6 1.0 SG A:CYS53 4.8 15.7 1.0 CD1 A:TYR30 5.0 23.2 1.0

Iron binding site 4 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe83 b:15.7 occ:1.00 FE4 A:SF483 0.0 15.7 1.0 S2 A:SF483 2.3 15.7 1.0 SG A:CYS53 2.3 15.7 1.0 S3 A:SF483 2.3 16.4 1.0 S1 A:SF483 2.3 15.3 1.0 FE1 A:SF483 2.7 16.2 1.0 FE2 A:SF483 2.7 16.2 1.0 FE3 A:SF483 2.7 15.4 1.0 CB A:CYS53 3.3 15.8 1.0 SG A:CYS57 3.6 17.5 1.0 CA A:CYS53 3.8 17.7 1.0 S4 A:SF483 3.9 15.7 1.0 CD A:PRO54 4.0 19.1 1.0 CD1 A:ILE58 4.4 15.7 1.0 CG1 A:ILE58 4.5 15.8 1.0 C A:CYS53 4.5 17.7 1.0 N A:PRO54 4.5 17.3 1.0 CG2 A:VAL55 4.6 18.6 1.0 SG A:CYS11 4.7 17.2 1.0 SG A:CYS14 4.8 16.3 1.0 SG A:CYS8 4.9 17.0 1.0 CG A:PRO54 4.9 22.1 1.0

Iron binding site 5 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:15.4 occ:1.00 FE1 A:SF484 0.0 15.4 1.0 S3 A:SF484 2.3 15.6 1.0 S2 A:SF484 2.3 15.4 1.0 S4 A:SF484 2.3 16.6 1.0 SG A:CYS37 2.3 15.7 1.0 FE4 A:SF484 2.7 15.6 1.0 FE3 A:SF484 2.7 15.1 1.0 FE2 A:SF484 2.8 15.7 1.0 CB A:CYS37 3.3 17.2 1.0 CA A:CYS37 3.7 16.3 1.0 N A:GLU39 3.8 15.7 1.0 S1 A:SF484 3.9 15.4 1.0 CA A:GLU39 4.1 15.7 1.0 N A:THR38 4.2 16.0 1.0 C A:CYS37 4.2 16.3 1.0 N A:CYS40 4.4 16.6 1.0 C A:GLU39 4.6 18.4 1.0 SG A:CYS49 4.7 15.6 1.0 SG A:CYS18 4.8 15.4 1.0 CG A:LEU2 4.9 14.8 1.0 CB A:ALA22 4.9 14.2 1.0 C A:THR38 4.9 17.2 1.0 N A:CYS37 5.0 15.3 1.0

Iron binding site 6 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:15.7 occ:1.00 FE2 A:SF484 0.0 15.7 1.0 S4 A:SF484 2.2 16.6 1.0 SG A:CYS40 2.3 17.1 1.0 S1 A:SF484 2.3 15.4 1.0 S3 A:SF484 2.3 15.6 1.0 FE4 A:SF484 2.7 15.6 1.0 FE3 A:SF484 2.8 15.1 1.0 FE1 A:SF484 2.8 15.4 1.0 N A:CYS40 3.3 16.6 1.0 CB A:CYS40 3.4 16.7 1.0 CA A:CYS40 3.6 15.6 1.0 C A:GLU39 3.9 18.4 1.0 S2 A:SF484 3.9 15.4 1.0 CA A:GLU39 4.2 15.7 1.0 N A:GLN48 4.3 16.1 1.0 CD A:PRO19 4.3 15.8 1.0 OG A:SER47 4.5 19.2 0.6 CA A:SER47 4.5 17.5 1.0 N A:GLU39 4.5 15.7 1.0 O A:GLU39 4.6 20.2 1.0 SG A:CYS18 4.7 15.4 1.0 SG A:CYS49 4.7 15.6 1.0 CB A:SER47 4.7 21.3 1.0 SG A:CYS37 4.8 15.7 1.0 OG1 A:THR38 4.8 17.4 1.0 C A:SER47 4.8 17.7 1.0 CG A:PRO19 4.9 17.4 1.0 N A:CYS49 4.9 15.8 1.0

Iron binding site 7 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:15.1 occ:1.00 FE3 A:SF484 0.0 15.1 1.0 S1 A:SF484 2.2 15.4 1.0 SG A:CYS49 2.3 15.6 1.0 S2 A:SF484 2.3 15.4 1.0 S4 A:SF484 2.3 16.6 1.0 FE4 A:SF484 2.7 15.6 1.0 FE1 A:SF484 2.7 15.4 1.0 FE2 A:SF484 2.8 15.7 1.0 CB A:CYS49 3.3 13.9 1.0 OG A:SER47 3.8 19.2 0.6 S3 A:SF484 3.9 15.6 1.0 N A:CYS49 4.0 15.8 1.0 CD1 A:ILE23 4.2 17.2 1.0 CA A:CYS49 4.2 13.9 1.0 SG A:CYS40 4.6 17.1 1.0 SG A:CYS37 4.7 15.7 1.0 CD1 A:LEU2 4.7 15.1 1.0 CD1 A:ILE32 4.7 15.4 1.0 SG A:CYS18 4.8 15.4 1.0 CB A:SER47 4.8 21.3 1.0 N A:GLN48 4.8 16.1 1.0 CG1 A:ILE23 5.0 14.5 1.0

Iron binding site 8 out of 8 in the Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the 2[4FE-4S] Ferredoxin V13G Variant From Allochromatium Vinosum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:15.6 occ:1.00 FE4 A:SF484 0.0 15.6 1.0 S2 A:SF484 2.3 15.4 1.0 S1 A:SF484 2.3 15.4 1.0 S3 A:SF484 2.3 15.6 1.0 SG A:CYS18 2.3 15.4 1.0 FE1 A:SF484 2.7 15.4 1.0 FE3 A:SF484 2.7 15.1 1.0 FE2 A:SF484 2.7 15.7 1.0 CB A:CYS18 3.2 14.6 1.0 CA A:CYS18 3.8 14.9 1.0 S4 A:SF484 3.8 16.6 1.0 CD A:PRO19 4.2 15.8 1.0 CB A:ALA22 4.2 14.2 1.0 SG A:CYS40 4.5 17.1 1.0 C A:CYS18 4.6 14.7 1.0 CD1 A:ILE23 4.6 17.2 1.0 N A:PRO19 4.7 14.7 1.0 SG A:CYS49 4.8 15.6 1.0 SG A:CYS37 4.8 15.7 1.0 CG1 A:ILE23 4.8 14.5 1.0 N A:ALA22 4.9 14.3 1.0 N A:CYS18 5.0 15.6 1.0

E.Saridakis, P.Giastas, G.Efthymiou, V.Thoma, J.M.Moulis, P.Kyritsis, I.M.Mavridis. Insight Into the Protein and Solvent Contributions to the Reduction Potentials of [4FE-4S]2+/+ Clusters: Crystal Structures of the Allochromatium Vinosum Ferredoxin Variants C57A and V13G and the Homologous Escherichia Coli Ferredoxin. J.Biol.Inorg.Chem. V. 14 783 2009.
ISSN: ISSN 0949-8257
PubMed: 19290553
DOI: 10.1007/S00775-009-0492-X