Iron in PDB 1xer: Structure of Ferredoxin

The structure of Structure of Ferredoxin, PDB code: 1xer was solved by T.Fujii, Y.Hata, H.Moriyama, T.Wakagi, N.Tanaka, T.Oshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.120, 50.120, 69.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 24.4

The structure of Structure of Ferredoxin also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Iron atom in the Structure of Ferredoxin (pdb code 1xer). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Ferredoxin, PDB code: 1xer:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:11.8 occ:1.00 FE1 A:F3S104 0.0 11.8 1.0 S2 A:F3S104 2.3 11.0 1.0 SG A:CYS45 2.3 6.2 1.0 S3 A:F3S104 2.3 9.4 1.0 S1 A:F3S104 2.3 8.9 1.0 FE3 A:F3S104 2.6 12.4 1.0 FE4 A:F3S104 2.6 12.3 1.0 CB A:CYS45 3.4 5.8 1.0 N A:ALA47 3.8 7.8 1.0 CA A:CYS45 3.9 6.7 1.0 S4 A:F3S104 3.9 7.3 1.0 N A:ILE46 4.1 8.6 1.0 CA A:ALA47 4.1 9.6 1.0 N A:ASP48 4.2 13.8 1.0 C A:CYS45 4.4 7.3 1.0 CB A:ALA75 4.5 8.0 1.0 C A:ALA47 4.6 12.8 1.0 SG A:CYS93 4.7 11.2 1.0 SG A:CYS51 4.7 10.2 1.0 N A:ALA75 4.8 8.3 1.0 N A:GLY49 4.8 12.0 1.0 C A:ILE46 4.9 7.5 1.0

Iron binding site 2 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:12.4 occ:1.00 FE3 A:F3S104 0.0 12.4 1.0 S1 A:F3S104 2.3 8.9 1.0 S4 A:F3S104 2.3 7.3 1.0 SG A:CYS93 2.3 11.2 1.0 S3 A:F3S104 2.3 9.4 1.0 FE4 A:F3S104 2.6 12.3 1.0 FE1 A:F3S104 2.6 11.8 1.0 CB A:CYS93 3.3 10.8 1.0 S2 A:F3S104 3.8 11.0 1.0 CA A:CYS93 3.9 14.7 1.0 CD A:PRO94 4.3 14.2 1.0 CG2 A:VAL95 4.5 9.7 1.0 CB A:ALA97 4.6 9.9 1.0 CB A:ASP48 4.6 10.2 1.0 C A:CYS93 4.6 13.4 1.0 SG A:CYS51 4.7 10.2 1.0 SG A:CYS45 4.7 6.2 1.0 N A:PRO94 4.7 14.6 1.0 CD1 A:ILE98 4.8 2.6 1.0 CG1 A:ILE98 4.9 5.1 1.0

Iron binding site 3 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe104 b:12.3 occ:1.00 FE4 A:F3S104 0.0 12.3 1.0 S4 A:F3S104 2.3 7.3 1.0 S2 A:F3S104 2.3 11.0 1.0 SG A:CYS51 2.3 10.2 1.0 S3 A:F3S104 2.3 9.4 1.0 FE3 A:F3S104 2.6 12.4 1.0 FE1 A:F3S104 2.6 11.8 1.0 CB A:CYS51 3.4 6.7 1.0 S1 A:F3S104 3.9 8.9 1.0 CB A:ALA75 3.9 8.0 1.0 N A:CYS51 4.0 9.3 1.0 N A:GLY49 4.1 12.0 1.0 CA A:CYS51 4.4 10.1 1.0 CD1 A:ILE98 4.4 2.6 1.0 CA A:GLY49 4.5 12.1 1.0 N A:SER50 4.6 9.0 1.0 SG A:CYS93 4.7 11.2 1.0 SG A:CYS45 4.7 6.2 1.0 C A:GLY49 4.8 9.6 1.0 N A:ASP48 5.0 13.8 1.0

Iron binding site 4 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:24.4 occ:1.00 FE1 A:F3S105 0.0 24.4 1.0 SG A:CYS83 2.3 17.5 1.0 S2 A:F3S105 2.3 25.5 1.0 S3 A:F3S105 2.3 24.9 1.0 S1 A:F3S105 2.3 23.2 1.0 FE4 A:F3S105 2.7 32.0 1.0 FE3 A:F3S105 2.7 20.8 1.0 CB A:CYS83 3.4 19.5 1.0 CA A:CYS83 3.8 18.5 1.0 S4 A:F3S105 4.0 19.1 1.0 N A:PHE85 4.0 24.2 1.0 N A:ILE84 4.1 15.5 1.0 N A:CYS86 4.2 31.6 1.0 CA A:PHE85 4.3 25.4 1.0 C A:CYS83 4.4 18.3 1.0 CG2 A:VAL59 4.4 4.3 1.0 CG2 A:VAL38 4.5 5.1 1.0 SG A:CYS89 4.7 26.9 1.0 SG A:CYS55 4.8 15.7 1.0 C A:PHE85 4.8 28.2 1.0 CG2 A:VAL100 4.9 10.7 1.0 C A:ILE84 5.0 22.2 1.0

Iron binding site 5 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:20.8 occ:1.00 FE3 A:F3S105 0.0 20.8 1.0 SG A:CYS55 2.3 15.7 1.0 S3 A:F3S105 2.3 24.9 1.0 S4 A:F3S105 2.3 19.1 1.0 S1 A:F3S105 2.3 23.2 1.0 FE4 A:F3S105 2.6 32.0 1.0 FE1 A:F3S105 2.7 24.4 1.0 CB A:CYS55 3.3 13.8 1.0 S2 A:F3S105 3.9 25.5 1.0 CA A:CYS55 3.9 16.9 1.0 CG2 A:VAL59 4.0 4.3 1.0 CD A:PRO56 4.3 15.5 1.0 CB A:VAL59 4.4 7.6 1.0 CG2 A:VAL57 4.5 11.5 1.0 CE2 A:PHE60 4.5 7.7 1.0 SG A:CYS89 4.7 26.9 1.0 C A:CYS55 4.8 15.8 1.0 N A:PRO56 4.8 16.0 1.0 SG A:CYS83 4.9 17.5 1.0 N A:CYS55 5.0 15.4 1.0

Iron binding site 6 out of 6 in the Structure of Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:32.0 occ:1.00 FE4 A:F3S105 0.0 32.0 1.0 S4 A:F3S105 2.3 19.1 1.0 SG A:CYS89 2.3 26.9 1.0 S3 A:F3S105 2.3 24.9 1.0 S2 A:F3S105 2.3 25.5 1.0 FE3 A:F3S105 2.6 20.8 1.0 FE1 A:F3S105 2.7 24.4 1.0 CB A:CYS89 3.3 28.1 1.0 N A:CYS89 3.9 26.9 1.0 S1 A:F3S105 3.9 23.2 1.0 CA A:CYS89 4.2 27.1 1.0 CE2 A:PHE60 4.5 7.7 1.0 CZ A:PHE60 4.5 7.2 1.0 CG2 A:VAL100 4.5 10.7 1.0 N A:ALA88 4.6 28.9 1.0 N A:MET87 4.6 30.9 1.0 SG A:CYS83 4.7 17.5 1.0 SG A:CYS55 4.7 15.7 1.0 N A:VAL90 5.0 23.4 1.0 CA A:MET87 5.0 31.8 1.0

T.Fujii, Y.Hata, T.Wakagi, N.Tanaka, T.Oshima. Novel Zinc-Binding Centre in Thermoacidophilic Archaeal Ferredoxins. Nat.Struct.Biol. V. 3 834 1996.
ISSN: ISSN 1072-8368
PubMed: 8836097
DOI: 10.1038/NSB1096-834