Iron in PDB 4dhv: Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster

The structure of Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster, PDB code: 4dhv was solved by I.N.Jakab-Simon, H.E.M.Christensen, L.T.Haahr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.66 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.110, 49.330, 54.390, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.7

The structure of Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster also contains other interesting chemical elements:

Silver	(Ag)	2 atoms
Cobalt	(Co)	4 atoms

The binding sites of Iron atom in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster (pdb code 4dhv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster, PDB code: 4dhv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:11.8 occ:1.00 FE1 B:0KA101 0.0 11.8 1.0 S1 B:0KA101 2.2 17.2 1.0 SG B:CYS56 2.2 11.5 1.0 S2 B:0KA101 2.3 14.0 1.0 S4 B:0KA101 2.3 13.1 1.0 FE2 B:0KA101 2.6 10.7 1.0 FE3 B:0KA101 2.7 13.5 1.0 O B:HOH249 2.9 30.9 1.0 AG1 B:0KA101 3.0 15.7 1.0 CB B:CYS56 3.5 15.9 1.0 S3 B:0KA101 3.9 16.4 1.0 CA B:CYS56 4.0 15.3 1.0 CD B:PRO57 4.3 15.9 1.0 CD1 B:ILE61 4.3 13.0 1.0 CB B:ALA60 4.5 15.0 1.0 CG1 B:ILE61 4.5 12.7 1.0 CG2 B:VAL58 4.6 6.4 1.0 N B:PRO57 4.7 15.3 1.0 C B:CYS56 4.7 15.5 1.0 SG B:CYS11 4.7 12.4 1.0 SG B:CYS17 4.8 11.4 1.0 N B:ALA60 4.9 15.9 1.0

Iron binding site 2 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:10.7 occ:1.00 FE2 B:0KA101 0.0 10.7 1.0 S4 B:0KA101 2.1 13.1 1.0 SG B:CYS11 2.3 12.4 1.0 S3 B:0KA101 2.3 16.4 1.0 S2 B:0KA101 2.3 14.0 1.0 FE1 B:0KA101 2.6 11.8 1.0 FE3 B:0KA101 2.6 13.5 1.0 AG1 B:0KA101 3.1 15.7 1.0 CB B:CYS11 3.2 12.8 1.0 CA B:CYS11 3.7 14.6 1.0 S1 B:0KA101 3.8 17.2 1.0 N B:ILE12 3.9 15.2 1.0 N B:GLY13 3.9 15.9 1.0 C B:CYS11 4.2 15.0 1.0 CB B:ALA33 4.2 15.8 1.0 O B:HOH249 4.3 30.9 1.0 CA B:GLY13 4.5 16.0 1.0 N B:ALA33 4.5 15.6 1.0 SG B:CYS56 4.6 11.5 1.0 SG B:CYS17 4.7 11.4 1.0 CG1 B:VAL6 4.8 15.9 1.0 N B:CYS14 4.8 17.0 1.0 CB B:ALA60 4.9 15.0 1.0 C B:ILE12 4.9 16.8 1.0

Iron binding site 3 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:13.5 occ:1.00 FE3 B:0KA101 0.0 13.5 1.0 S1 B:0KA101 2.2 17.2 1.0 S2 B:0KA101 2.2 14.0 1.0 S3 B:0KA101 2.3 16.4 1.0 SG B:CYS17 2.3 11.4 1.0 FE2 B:0KA101 2.6 10.7 1.0 FE1 B:0KA101 2.7 11.8 1.0 CB B:CYS17 3.2 9.3 1.0 AG1 B:0KA101 3.3 15.7 1.0 CB B:ALA33 3.6 15.8 1.0 O B:HOH249 3.6 30.9 1.0 S4 B:0KA101 3.9 13.1 1.0 N B:CYS17 4.0 9.4 1.0 CD1 B:ILE61 4.1 13.0 1.0 CA B:CYS17 4.3 9.7 1.0 SG B:CYS11 4.6 12.4 1.0 N B:ALA15 4.6 13.6 1.0 CA B:ALA15 4.6 12.0 1.0 SG B:CYS56 4.7 11.5 1.0 N B:ILE16 4.7 10.4 1.0 CG1 B:ILE61 4.8 12.7 1.0 C B:ALA15 4.9 12.1 1.0 CA B:ALA33 5.0 15.4 1.0

Iron binding site 4 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:18.5 occ:1.00 FE1 A:0KA102 0.0 18.5 1.0 S1 A:0KA102 2.3 12.5 1.0 SG A:CYS56 2.3 15.1 1.0 S4 A:0KA102 2.3 18.2 1.0 S2 A:0KA102 2.4 13.1 1.0 FE3 A:0KA102 2.7 14.1 1.0 FE2 A:0KA102 2.7 14.1 1.0 AG1 A:0KA102 3.0 18.8 1.0 CB A:CYS56 3.4 17.0 1.0 S3 A:0KA102 3.7 15.5 1.0 CA A:CYS56 3.9 16.3 1.0 CD A:PRO57 4.0 16.4 1.0 CB A:ALA60 4.3 15.3 1.0 N A:PRO57 4.6 16.7 1.0 C A:CYS56 4.6 17.1 1.0 CG1 A:ILE61 4.6 13.1 1.0 CD1 A:ILE61 4.7 17.7 1.0 SG A:CYS11 4.8 15.7 1.0 CG A:PRO57 4.8 18.4 1.0 SG A:CYS17 4.8 14.1 1.0 CG2 A:VAL58 5.0 16.9 1.0 N A:ALA60 5.0 16.9 1.0

Iron binding site 5 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:14.1 occ:1.00 FE2 A:0KA102 0.0 14.1 1.0 S2 A:0KA102 2.2 13.1 1.0 SG A:CYS11 2.2 15.7 1.0 S3 A:0KA102 2.2 15.5 1.0 S4 A:0KA102 2.3 18.2 1.0 FE3 A:0KA102 2.6 14.1 1.0 FE1 A:0KA102 2.7 18.5 1.0 AG1 A:0KA102 3.1 18.8 1.0 CB A:CYS11 3.4 18.7 1.0 CA A:CYS11 3.8 18.8 1.0 N A:GLY13 3.9 18.2 1.0 N A:ILE12 3.9 19.1 1.0 CB A:ALA33 4.0 16.7 1.0 S1 A:0KA102 4.0 12.5 1.0 C A:CYS11 4.2 19.1 1.0 N A:ALA33 4.4 17.9 1.0 CA A:GLY13 4.4 18.1 1.0 CB A:ALA60 4.6 15.3 1.0 SG A:CYS56 4.7 15.1 1.0 CG1 A:VAL6 4.8 20.3 1.0 SG A:CYS17 4.8 14.1 1.0 N A:CYS14 4.8 17.8 1.0 CA A:ALA33 4.9 17.1 1.0 C A:ILE12 4.9 18.0 1.0 CA A:ILE12 5.0 18.6 1.0

Iron binding site 6 out of 6 in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster


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 Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe102 b:14.1 occ:1.00 FE3 A:0KA102 0.0 14.1 1.0 S3 A:0KA102 2.1 15.5 1.0 S2 A:0KA102 2.4 13.1 1.0 SG A:CYS17 2.4 14.1 1.0 S1 A:0KA102 2.4 12.5 1.0 FE2 A:0KA102 2.6 14.1 1.0 FE1 A:0KA102 2.7 18.5 1.0 AG1 A:0KA102 3.3 18.8 1.0 CB A:CYS17 3.4 12.4 1.0 CB A:ALA33 3.5 16.7 1.0 N A:CYS17 3.9 13.1 1.0 S4 A:0KA102 4.0 18.2 1.0 CA A:CYS17 4.3 12.3 1.0 CD1 A:ILE61 4.4 17.7 1.0 SG A:CYS11 4.5 15.7 1.0 N A:ILE16 4.6 13.9 1.0 N A:ALA15 4.7 13.9 1.0 CA A:ALA15 4.8 14.2 1.0 CA A:ALA33 4.8 17.1 1.0 SG A:CYS56 4.8 15.1 1.0 C A:ALA15 4.9 14.0 1.0 CG1 A:ILE61 4.9 13.1 1.0 C A:ILE16 5.0 13.3 1.0

M.Martic, I.N.Jakab-Simon, L.T.Haahr, W.R.Hagen, H.E.Christensen. Heterometallic [Agfe(3)S (4)] Ferredoxin Variants: Synthesis, Characterization, and the First Crystal Structure of An Engineered Heterometallic Iron-Sulfur Protein. J.Biol.Inorg.Chem. V. 18 261 2013.
ISSN: ISSN 0949-8257
PubMed: 23296387
DOI: 10.1007/S00775-012-0971-3