Iron in PDB 2zvs: Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli

The structure of Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli, PDB code: 2zvs was solved by P.Giastas, M.I.Mavridis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.65
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	65.543, 65.543, 132.367, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 27.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli (pdb code 2zvs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli, PDB code: 2zvs:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:22.5 occ:1.00 FE1 A:SF4101 0.0 22.5 1.0 S4 A:SF4101 2.3 21.2 1.0 S3 A:SF4101 2.3 30.0 1.0 S2 A:SF4101 2.3 22.6 1.0 SG A:CYS8 2.3 20.7 1.0 FE4 A:SF4101 2.6 21.8 1.0 FE2 A:SF4101 2.7 23.1 1.0 FE3 A:SF4101 2.8 24.9 1.0 CB A:CYS8 3.1 14.4 1.0 CA A:CYS8 3.7 18.8 1.0 N A:ILE9 3.8 18.3 1.0 S1 A:SF4101 3.8 26.0 1.0 C A:CYS8 4.1 20.0 1.0 CG2 A:ILE4 4.2 41.4 1.0 N A:ASN10 4.3 20.6 1.0 CB A:TYR30 4.7 45.4 1.0 CA A:ASN10 4.8 30.5 1.0 ND2 A:ASN57 4.8 18.8 1.0 SG A:CYS53 4.8 23.6 1.0 SG A:CYS14 4.9 18.7 1.0 CD2 A:TYR30 4.9 43.2 1.0 N A:CYS11 4.9 20.7 1.0 SG A:CYS11 4.9 32.3 1.0

Iron binding site 2 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:23.1 occ:1.00 FE2 A:SF4101 0.0 23.1 1.0 SG A:CYS11 2.3 32.3 1.0 S4 A:SF4101 2.3 21.2 1.0 S3 A:SF4101 2.3 30.0 1.0 S1 A:SF4101 2.3 26.0 1.0 FE4 A:SF4101 2.7 21.8 1.0 FE1 A:SF4101 2.7 22.5 1.0 FE3 A:SF4101 2.8 24.9 1.0 CB A:CYS11 3.5 39.5 1.0 N A:CYS11 3.6 20.7 1.0 S2 A:SF4101 3.9 22.6 1.0 CA A:CYS11 4.0 29.3 1.0 CD A:PRO54 4.0 33.1 1.0 N A:ASP12 4.2 19.4 1.0 C A:CYS11 4.2 18.7 1.0 CG A:PRO54 4.5 14.9 1.0 N A:MET13 4.5 31.9 1.0 SG A:CYS8 4.6 20.7 1.0 CB A:MET13 4.6 23.2 1.0 C A:ASN10 4.7 28.2 1.0 SG A:CYS53 4.7 23.6 1.0 SG A:CYS14 4.8 18.7 1.0 N A:ASN10 4.8 20.6 1.0 N A:ILE9 4.9 18.3 1.0 CA A:ASN10 4.9 30.5 1.0 CG1 A:ILE9 4.9 10.1 1.0 N A:CYS14 5.0 23.4 1.0

Iron binding site 3 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:24.9 occ:1.00 FE3 A:SF4101 0.0 24.9 1.0 SG A:CYS14 2.2 18.7 1.0 S1 A:SF4101 2.3 26.0 1.0 S4 A:SF4101 2.3 21.2 1.0 S2 A:SF4101 2.3 22.6 1.0 FE4 A:SF4101 2.8 21.8 1.0 FE2 A:SF4101 2.8 23.1 1.0 FE1 A:SF4101 2.8 22.5 1.0 CB A:CYS14 3.1 16.0 1.0 S3 A:SF4101 4.0 30.0 1.0 N A:CYS14 4.0 23.4 1.0 CA A:CYS14 4.2 28.1 1.0 SG A:CYS11 4.6 32.3 1.0 SG A:CYS8 4.7 20.7 1.0 CD2 A:TYR30 4.7 43.2 1.0 CB A:TYR30 4.7 45.4 1.0 CG A:TYR30 4.8 47.3 1.0 SG A:CYS53 4.8 23.6 1.0 CD1 A:ILE4 4.9 9.2 1.0

Iron binding site 4 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:21.8 occ:1.00 FE4 A:SF4101 0.0 21.8 1.0 S2 A:SF4101 2.3 22.6 1.0 S1 A:SF4101 2.3 26.0 1.0 S3 A:SF4101 2.3 30.0 1.0 SG A:CYS53 2.3 23.6 1.0 FE1 A:SF4101 2.6 22.5 1.0 FE2 A:SF4101 2.7 23.1 1.0 FE3 A:SF4101 2.8 24.9 1.0 CB A:CYS53 3.7 13.9 1.0 S4 A:SF4101 3.8 21.2 1.0 CD A:PRO54 3.9 33.1 1.0 CA A:CYS53 4.0 22.4 1.0 ND2 A:ASN57 4.6 18.8 1.0 N A:PRO54 4.6 19.1 1.0 SG A:CYS11 4.6 32.3 1.0 C A:CYS53 4.7 28.6 1.0 CB A:ASN57 4.7 44.9 1.0 CG A:ASN57 4.8 47.8 1.0 CG1 A:ILE55 4.8 16.3 1.0 CG A:PRO54 4.8 14.9 1.0 SG A:CYS14 4.9 18.7 1.0 OG1 A:THR58 4.9 29.5 1.0 SG A:CYS8 4.9 20.7 1.0

Iron binding site 5 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:19.4 occ:1.00 FE1 A:SF4102 0.0 19.4 1.0 S4 A:SF4102 2.3 15.9 1.0 S2 A:SF4102 2.3 19.5 1.0 S3 A:SF4102 2.3 27.7 1.0 SG A:CYS37 2.3 21.5 1.0 FE4 A:SF4102 2.6 21.9 1.0 FE2 A:SF4102 2.7 21.2 1.0 FE3 A:SF4102 2.7 20.4 1.0 CB A:CYS37 3.3 22.3 1.0 S1 A:SF4102 3.9 27.6 1.0 CA A:CYS37 3.9 22.6 1.0 N A:GLU39 3.9 17.3 1.0 CA A:GLU39 4.0 14.1 1.0 N A:THR38 4.3 16.9 1.0 C A:CYS37 4.5 13.4 1.0 N A:CYS40 4.6 27.9 1.0 CG A:LEU2 4.6 13.6 1.0 SG A:CYS18 4.7 18.0 1.0 SG A:CYS49 4.7 20.7 1.0 C A:GLU39 4.7 28.6 1.0 CB A:LEU2 4.8 15.2 1.0 CG2 A:ILE32 4.8 12.7 1.0 SG A:CYS40 4.9 16.3 1.0 CD1 A:LEU2 4.9 13.6 1.0 N A:LEU2 5.0 17.1 1.0

Iron binding site 6 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:21.2 occ:1.00 FE2 A:SF4102 0.0 21.2 1.0 S3 A:SF4102 2.3 27.7 1.0 S4 A:SF4102 2.3 15.9 1.0 S1 A:SF4102 2.3 27.6 1.0 SG A:CYS40 2.3 16.3 1.0 FE4 A:SF4102 2.6 21.9 1.0 FE1 A:SF4102 2.7 19.4 1.0 FE3 A:SF4102 2.7 20.4 1.0 N A:CYS40 3.5 27.9 1.0 CB A:CYS40 3.6 16.4 1.0 CA A:CYS40 3.8 26.6 1.0 S2 A:SF4102 3.8 19.5 1.0 C A:GLU39 4.0 28.6 1.0 N A:THR48 4.2 24.2 1.0 CA A:GLU39 4.2 14.1 1.0 CD A:PRO19 4.2 15.3 1.0 SG A:CYS49 4.5 20.7 1.0 CA A:PRO47 4.5 32.7 1.0 SG A:CYS18 4.5 18.0 1.0 N A:GLU39 4.6 17.3 1.0 SG A:CYS37 4.7 21.5 1.0 C A:PRO47 4.7 17.7 1.0 O A:GLU39 4.8 18.7 1.0 CB A:PRO47 4.8 21.9 1.0 N A:CYS49 4.9 28.9 1.0 CG A:PRO19 4.9 20.3 1.0 OG1 A:THR48 4.9 21.2 1.0

Iron binding site 7 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:20.4 occ:1.00 FE3 A:SF4102 0.0 20.4 1.0 SG A:CYS49 2.3 20.7 1.0 S1 A:SF4102 2.3 27.6 1.0 S4 A:SF4102 2.3 15.9 1.0 S2 A:SF4102 2.3 19.5 1.0 FE4 A:SF4102 2.7 21.9 1.0 FE2 A:SF4102 2.7 21.2 1.0 FE1 A:SF4102 2.7 19.4 1.0 CB A:CYS49 3.4 28.0 1.0 N A:CYS49 3.8 28.9 1.0 S3 A:SF4102 3.9 27.7 1.0 CA A:CYS49 4.3 27.7 1.0 CD1 A:LEU2 4.5 13.6 1.0 CD1 A:ILE23 4.6 20.2 1.0 SG A:CYS40 4.6 16.3 1.0 SG A:CYS37 4.7 21.5 1.0 SG A:CYS18 4.7 18.0 1.0 N A:THR48 4.8 24.2 1.0 CD1 A:ILE32 4.9 17.0 1.0 CG1 A:ILE23 5.0 41.8 1.0 CB A:CYS18 5.0 15.1 1.0 C A:THR48 5.0 19.7 1.0 CB A:PRO47 5.0 21.9 1.0 CG A:LEU2 5.0 13.6 1.0

Iron binding site 8 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


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 From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:21.9 occ:1.00 FE4 A:SF4102 0.0 21.9 1.0 S2 A:SF4102 2.3 19.5 1.0 SG A:CYS18 2.3 18.0 1.0 S1 A:SF4102 2.3 27.6 1.0 S3 A:SF4102 2.3 27.7 1.0 FE2 A:SF4102 2.6 21.2 1.0 FE1 A:SF4102 2.6 19.4 1.0 FE3 A:SF4102 2.7 20.4 1.0 CB A:CYS18 3.2 15.1 1.0 S4 A:SF4102 3.8 15.9 1.0 CA A:CYS18 3.9 15.0 1.0 CD A:PRO19 4.3 15.3 1.0 SG A:CYS40 4.6 16.3 1.0 C A:CYS18 4.6 14.3 1.0 CB A:ALA22 4.6 20.0 1.0 CG1 A:ILE23 4.6 41.8 1.0 N A:PRO19 4.8 21.7 1.0 SG A:CYS37 4.8 21.5 1.0 SG A:CYS49 4.8 20.7 1.0 CD1 A:ILE23 4.9 20.2 1.0

Iron binding site 9 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:31.6 occ:1.00 FE1 B:SF4203 0.0 31.6 1.0 S4 B:SF4203 2.3 35.3 1.0 SG B:CYS8 2.3 32.6 1.0 S3 B:SF4203 2.3 37.2 1.0 S2 B:SF4203 2.3 28.5 1.0 FE4 B:SF4203 2.7 30.1 1.0 FE3 B:SF4203 2.7 34.1 1.0 FE2 B:SF4203 2.8 31.9 1.0 CB B:CYS8 3.5 13.7 1.0 OD1 B:ASN57 3.6 72.7 1.0 CA B:CYS8 3.8 25.8 1.0 S1 B:SF4203 3.9 34.9 1.0 N B:ILE9 4.0 38.8 1.0 N B:ASN10 4.0 48.9 1.0 C B:CYS8 4.3 30.7 1.0 CB B:TYR30 4.4 27.7 1.0 CA B:ASN10 4.4 40.0 1.0 CG B:ASN57 4.6 46.7 1.0 SG B:CYS53 4.6 29.0 1.0 CD1 B:TYR30 4.6 25.0 1.0 SG B:CYS14 4.8 30.5 1.0 CG B:TYR30 4.8 17.4 1.0 SG B:CYS11 4.8 49.2 1.0 N B:CYS11 4.9 25.0 1.0 CG2 B:ILE4 4.9 27.8 1.0 C B:ILE9 5.0 51.8 1.0

Iron binding site 10 out of 24 in the Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the 2[4FE-4S] Ferredoxin From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:31.9 occ:1.00 FE2 B:SF4203 0.0 31.9 1.0 S4 B:SF4203 2.3 35.3 1.0 S3 B:SF4203 2.3 37.2 1.0 S1 B:SF4203 2.3 34.9 1.0 SG B:CYS11 2.3 49.2 1.0 FE4 B:SF4203 2.6 30.1 1.0 FE3 B:SF4203 2.7 34.1 1.0 FE1 B:SF4203 2.8 31.6 1.0 N B:ASP12 3.6 30.1 1.0 N B:CYS11 3.6 25.0 1.0 CB B:CYS11 3.7 21.1 1.0 S2 B:SF4203 3.9 28.5 1.0 CA B:CYS11 3.9 27.6 1.0 C B:CYS11 3.9 31.6 1.0 CD B:PRO54 4.1 35.2 1.0 N B:MET13 4.5 32.9 1.0 N B:ASN10 4.5 48.9 1.0 CA B:ASP12 4.5 22.7 1.0 C B:ASN10 4.5 42.2 1.0 CG B:PRO54 4.7 24.9 1.0 SG B:CYS14 4.7 30.5 1.0 CA B:ASN10 4.7 40.0 1.0 SG B:CYS53 4.7 29.0 1.0 SG B:CYS8 4.7 32.6 1.0 O B:CYS11 4.8 37.8 1.0 N B:CYS14 4.9 19.8 1.0 C B:ASP12 4.9 24.5 1.0 CA B:CYS53 4.9 26.0 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