Silver 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:

Cobalt	(Co)	4 atoms
Iron	(Fe)	6 atoms

The binding sites of Silver 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 Silver atom.
In total 2 binding sites of Silver where determined in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster, PDB code: 4dhv:
Jump to Silver binding site number: 1; 2;

Silver binding site 1 out of 2 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 Silver with other atoms in the Ag 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:Ag101 b:15.7 occ:1.00 AG1 B:0KA101 0.0 15.7 1.0 O B:HOH249 1.8 30.9 1.0 SG B:CYS14 2.3 11.8 1.0 S4 B:0KA101 2.6 13.1 1.0 S3 B:0KA101 2.8 16.4 1.0 S1 B:0KA101 2.8 17.2 1.0 FE1 B:0KA101 3.0 11.8 1.0 FE2 B:0KA101 3.1 10.7 1.0 FE3 B:0KA101 3.3 13.5 1.0 CB B:CYS14 3.4 17.4 1.0 N B:CYS14 3.4 17.0 1.0 N B:ALA15 3.6 13.6 1.0 CA B:CYS14 3.7 15.5 1.0 CD B:PRO57 3.8 15.9 1.0 C B:CYS14 4.0 15.0 1.0 CG B:PRO57 4.1 16.5 1.0 N B:ILE16 4.2 10.4 1.0 CG2 B:ILE16 4.4 13.6 1.0 C B:GLY13 4.5 15.4 1.0 S2 B:0KA101 4.5 14.0 1.0 N B:GLY13 4.5 15.9 1.0 CG1 B:ILE12 4.5 17.5 1.0 CA B:ALA15 4.5 12.0 1.0 SG B:CYS56 4.7 11.5 1.0 CA B:GLY13 4.8 16.0 1.0 C B:ALA15 4.8 12.1 1.0 N B:PRO57 5.0 15.3 1.0 SG B:CYS11 5.0 12.4 1.0 N B:ILE12 5.0 15.2 1.0

Silver binding site 2 out of 2 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 Silver with other atoms in the Ag 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 A:Ag102 b:18.8 occ:1.00 AG1 A:0KA102 0.0 18.8 1.0 SG A:CYS14 2.4 21.5 1.0 S4 A:0KA102 2.5 18.2 1.0 S3 A:0KA102 2.7 15.5 1.0 S1 A:0KA102 2.8 12.5 1.0 FE1 A:0KA102 3.0 18.5 1.0 FE2 A:0KA102 3.1 14.1 1.0 FE3 A:0KA102 3.3 14.1 1.0 N A:CYS14 3.4 17.8 1.0 CB A:CYS14 3.6 17.5 1.0 N A:ALA15 3.8 13.9 1.0 CA A:CYS14 3.9 17.6 1.0 CD A:PRO57 3.9 16.4 1.0 CG A:PRO57 4.1 18.4 1.0 N A:ILE16 4.1 13.9 1.0 C A:CYS14 4.1 17.1 1.0 CG1 A:ILE12 4.2 18.3 1.0 N A:GLY13 4.3 18.2 1.0 C A:GLY13 4.4 18.2 1.0 S2 A:0KA102 4.5 13.1 1.0 CB A:ILE16 4.6 15.0 1.0 CA A:GLY13 4.7 18.1 1.0 CA A:ALA15 4.7 14.2 1.0 SG A:CYS56 4.8 15.1 1.0 N A:ILE12 4.8 19.1 1.0 C A:ILE12 4.9 18.0 1.0 CD1 A:ILE12 4.9 21.8 1.0 C A:ALA15 4.9 14.0 1.0 CA A:ILE16 4.9 13.8 1.0 SG A:CYS11 4.9 15.7 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