Iron in PDB 2z8q: Ferredoxin From Pyrococcus Furiosus, D14C Variant

The structure of Ferredoxin From Pyrococcus Furiosus, D14C Variant, PDB code: 2z8q was solved by M.N.Johannessen, H.E.M.Christensen, P.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.01 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.400, 116.800, 47.700, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.4

The structure of Ferredoxin From Pyrococcus Furiosus, D14C Variant also contains other interesting chemical elements:

Cobalt

(Co)

5 atoms

The binding sites of Iron atom in the Ferredoxin From Pyrococcus Furiosus, D14C Variant (pdb code 2z8q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Ferredoxin From Pyrococcus Furiosus, D14C Variant, PDB code: 2z8q:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.7 occ:1.00 FE1 A:SF4101 0.0 2.7 1.0 S2 A:SF4101 2.3 5.8 1.0 SG A:CYS17 2.3 2.0 0.9 S4 A:SF4101 2.3 3.7 1.0 S3 A:SF4101 2.4 3.4 1.0 FE3 A:SF4101 2.7 3.5 1.0 FE2 A:SF4101 2.7 2.6 1.0 FE4 A:SF4101 2.7 2.7 1.0 SG A:CYS17 2.8 2.0 0.1 CB A:CYS17 3.2 2.0 0.1 CB A:CYS17 3.2 5.3 0.9 CB A:ALA33 3.8 3.8 1.0 N A:CYS17 3.9 2.0 0.1 N A:CYS17 3.9 2.0 0.9 S1 A:SF4101 3.9 4.5 1.0 CA A:CYS17 4.2 2.0 0.1 CA A:CYS17 4.2 3.4 0.9 CD1 A:ILE61 4.4 2.0 1.0 SG A:CYS14 4.7 3.8 1.0 SG A:CYS11 4.7 3.5 1.0 N A:ILE16 4.8 2.0 1.0 N A:ALA15 4.8 2.0 1.0 SG A:CYS56 4.8 2.0 1.0 CG1 A:ILE61 4.9 7.7 1.0 CA A:ALA15 5.0 3.6 1.0

Iron binding site 2 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.6 occ:1.00 FE2 A:SF4101 0.0 2.6 1.0 SG A:CYS11 2.3 3.5 1.0 S4 A:SF4101 2.3 3.7 1.0 S1 A:SF4101 2.3 4.5 1.0 S3 A:SF4101 2.3 3.4 1.0 FE1 A:SF4101 2.7 2.7 1.0 FE4 A:SF4101 2.8 2.7 1.0 FE3 A:SF4101 2.8 3.5 1.0 CB A:CYS11 3.3 2.0 1.0 CA A:CYS11 3.8 2.0 1.0 N A:ILE12 3.9 2.0 1.0 N A:GLY13 3.9 3.3 1.0 S2 A:SF4101 3.9 5.8 1.0 CB A:ALA33 4.2 3.8 1.0 C A:CYS11 4.3 3.9 1.0 N A:ALA33 4.5 2.0 1.0 CA A:GLY13 4.5 2.0 1.0 CG1 A:VAL6 4.6 2.3 1.0 N A:CYS14 4.6 2.0 1.0 SG A:CYS56 4.7 2.0 1.0 SG A:CYS17 4.8 2.0 0.9 CB A:ALA60 4.8 3.3 1.0 C A:ILE12 4.9 4.9 1.0 CA A:ALA33 5.0 2.0 1.0 SG A:CYS14 5.0 3.8 1.0

Iron binding site 3 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:3.5 occ:1.00 FE3 A:SF4101 0.0 3.5 1.0 SG A:CYS14 2.3 3.8 1.0 S4 A:SF4101 2.3 3.7 1.0 S2 A:SF4101 2.3 5.8 1.0 S1 A:SF4101 2.3 4.5 1.0 FE1 A:SF4101 2.7 2.7 1.0 FE4 A:SF4101 2.7 2.7 1.0 FE2 A:SF4101 2.8 2.6 1.0 N A:CYS14 3.5 2.0 1.0 CB A:CYS14 3.5 6.4 1.0 N A:ALA15 3.7 2.0 1.0 CA A:CYS14 3.8 3.0 1.0 S3 A:SF4101 4.0 3.4 1.0 C A:CYS14 4.1 7.2 1.0 N A:ILE16 4.2 2.0 1.0 CD A:PRO57 4.3 2.0 1.0 C A:GLY13 4.5 3.8 1.0 N A:GLY13 4.6 3.3 1.0 SG A:CYS56 4.6 2.0 1.0 CA A:ALA15 4.6 3.6 1.0 CG A:PRO57 4.6 4.0 1.0 SG A:CYS17 4.6 2.0 0.1 SG A:CYS17 4.7 2.0 0.9 CB A:ILE16 4.7 2.9 1.0 SG A:CYS11 4.7 3.5 1.0 CA A:GLY13 4.8 2.0 1.0 CG1 A:ILE12 4.8 4.4 1.0 N A:CYS17 4.8 2.0 0.9 N A:CYS17 4.8 2.0 0.1 C A:ALA15 4.9 2.0 1.0

Iron binding site 4 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.7 occ:1.00 FE4 A:SF4101 0.0 2.7 1.0 SG A:CYS56 2.2 2.0 1.0 S2 A:SF4101 2.3 5.8 1.0 S3 A:SF4101 2.3 3.4 1.0 S1 A:SF4101 2.3 4.5 1.0 FE3 A:SF4101 2.7 3.5 1.0 FE1 A:SF4101 2.7 2.7 1.0 FE2 A:SF4101 2.8 2.6 1.0 CB A:CYS56 3.2 2.7 1.0 SG A:CYS17 3.8 2.0 0.1 CA A:CYS56 3.9 2.9 1.0 S4 A:SF4101 3.9 3.7 1.0 CD A:PRO57 4.3 2.0 1.0 CD1 A:ILE61 4.4 2.0 1.0 CB A:ALA60 4.4 3.3 1.0 CG2 A:VAL58 4.5 2.0 1.0 CG1 A:ILE61 4.5 7.7 1.0 C A:CYS56 4.6 2.7 1.0 SG A:CYS14 4.6 3.8 1.0 N A:PRO57 4.6 2.0 1.0 N A:ALA60 4.8 2.0 1.0 SG A:CYS17 4.9 2.0 0.9 SG A:CYS11 4.9 3.5 1.0 CG A:PRO57 5.0 4.0 1.0

Iron binding site 5 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:8.6 occ:1.00 FE1 B:SF4101 0.0 8.6 1.0 S2 B:SF4101 2.3 9.1 1.0 S4 B:SF4101 2.3 10.3 1.0 SG B:CYS17 2.3 8.1 1.0 S3 B:SF4101 2.3 11.2 1.0 FE2 B:SF4101 2.7 10.1 1.0 FE4 B:SF4101 2.7 9.1 1.0 FE3 B:SF4101 2.7 8.8 1.0 CB B:CYS17 3.2 6.7 1.0 CB B:ALA33 3.6 12.3 1.0 N B:CYS17 3.8 5.5 1.0 S1 B:SF4101 3.9 11.7 1.0 CA B:CYS17 4.2 6.7 1.0 CD1 B:ILE61 4.3 10.4 1.0 SG B:CYS11 4.7 10.6 1.0 N B:ILE16 4.7 5.5 1.0 SG B:CYS56 4.7 10.8 1.0 SG B:CYS14 4.7 9.2 1.0 N B:ALA15 4.8 5.4 1.0 CA B:ALA15 4.9 3.4 1.0 CG1 B:ILE61 4.9 8.6 1.0 C B:ALA15 5.0 4.3 1.0 C B:ILE16 5.0 6.0 1.0

Iron binding site 6 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:10.1 occ:1.00 FE2 B:SF4101 0.0 10.1 1.0 SG B:CYS11 2.3 10.6 1.0 S1 B:SF4101 2.3 11.7 1.0 S4 B:SF4101 2.3 10.3 1.0 S3 B:SF4101 2.3 11.2 1.0 FE1 B:SF4101 2.7 8.6 1.0 FE3 B:SF4101 2.7 8.8 1.0 FE4 B:SF4101 2.7 9.1 1.0 CB B:CYS11 3.3 13.4 1.0 CA B:CYS11 3.7 12.8 1.0 S2 B:SF4101 3.9 9.1 1.0 N B:ILE12 3.9 10.1 1.0 N B:GLY13 4.0 7.5 1.0 CB B:ALA33 4.1 12.3 1.0 C B:CYS11 4.2 12.2 1.0 N B:ALA33 4.6 12.8 1.0 CA B:GLY13 4.6 6.3 1.0 N B:CYS14 4.7 10.2 1.0 SG B:CYS56 4.8 10.8 1.0 SG B:CYS17 4.8 8.1 1.0 CB B:ALA60 4.8 10.3 1.0 CG1 B:VAL6 4.9 13.3 1.0 SG B:CYS14 4.9 9.2 1.0 C B:ILE12 5.0 9.6 1.0 N B:CYS11 5.0 14.9 1.0

Iron binding site 7 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:8.8 occ:1.00 FE3 B:SF4101 0.0 8.8 1.0 SG B:CYS14 2.3 9.2 1.0 S1 B:SF4101 2.3 11.7 1.0 S4 B:SF4101 2.3 10.3 1.0 S2 B:SF4101 2.3 9.1 1.0 FE4 B:SF4101 2.7 9.1 1.0 FE2 B:SF4101 2.7 10.1 1.0 FE1 B:SF4101 2.7 8.6 1.0 CB B:CYS14 3.5 6.0 1.0 N B:CYS14 3.6 10.2 1.0 N B:ALA15 3.6 5.4 1.0 CA B:CYS14 3.9 9.6 1.0 S3 B:SF4101 3.9 11.2 1.0 N B:ILE16 4.1 5.5 1.0 C B:CYS14 4.1 8.9 1.0 CD B:PRO57 4.2 9.8 1.0 CA B:ALA15 4.5 3.4 1.0 N B:GLY13 4.5 7.5 1.0 SG B:CYS56 4.6 10.8 1.0 C B:GLY13 4.6 5.9 1.0 SG B:CYS11 4.7 10.6 1.0 C B:ALA15 4.8 4.3 1.0 CB B:ILE16 4.8 6.5 1.0 SG B:CYS17 4.8 8.1 1.0 CG B:PRO57 4.8 9.7 1.0 N B:CYS17 4.8 5.5 1.0 CG1 B:ILE12 4.9 12.5 1.0 CA B:GLY13 4.9 6.3 1.0 CA B:ILE16 5.0 7.0 1.0

Iron binding site 8 out of 8 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:9.1 occ:1.00 FE4 B:SF4101 0.0 9.1 1.0 SG B:CYS56 2.2 10.8 1.0 S1 B:SF4101 2.3 11.7 1.0 S2 B:SF4101 2.3 9.1 1.0 S3 B:SF4101 2.3 11.2 1.0 FE1 B:SF4101 2.7 8.6 1.0 FE3 B:SF4101 2.7 8.8 1.0 FE2 B:SF4101 2.7 10.1 1.0 CB B:CYS56 3.3 9.8 1.0 S4 B:SF4101 3.9 10.3 1.0 CA B:CYS56 3.9 8.2 1.0 CD B:PRO57 4.1 9.8 1.0 CB B:ALA60 4.2 10.3 1.0 CG2 B:VAL58 4.5 10.6 1.0 CD1 B:ILE61 4.6 10.4 1.0 SG B:CYS14 4.6 9.2 1.0 C B:CYS56 4.6 8.9 1.0 N B:PRO57 4.6 9.3 1.0 CG1 B:ILE61 4.8 8.6 1.0 SG B:CYS17 4.8 8.1 1.0 N B:ALA60 4.8 11.4 1.0 SG B:CYS11 4.9 10.6 1.0

M.N.Johannessen, M.S.Nielsen, B.L.Ooi, H.E.M.Christensen, P.Harris. The Crystal Structure of the All Cysteinyl Coordinated D14C Variant of [4FE-4S] Pyrococcus Furiosus Ferredoxin To Be Published.