Cobalt 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
Iron	(Fe)	6 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of the Pyrococcus Furiosus Ferredoxin D14C Variant Containing the Heterometallic [AGFE3S4] Cluster, PDB code: 4dhv:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 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 Cobalt with other atoms in the Co 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:Co102 b:30.1 occ:1.00 CO B:NCO102 0.0 30.1 1.0 N2 B:NCO102 1.9 22.7 1.0 N3 B:NCO102 2.0 29.7 1.0 N1 B:NCO102 2.0 28.0 1.0 N6 B:NCO102 2.0 24.8 1.0 N5 B:NCO102 2.2 15.9 1.0 N4 B:NCO102 2.3 21.3 1.0 O A:LEU20 3.8 15.5 1.0 OE2 B:GLU41 4.2 25.9 1.0 OE1 B:GLU41 4.3 26.2 1.0 O B:HOH215 4.3 25.8 1.0 OD2 B:ASP42 4.3 21.0 1.0 OE1 B:GLU43 4.4 24.1 1.0 CD B:GLU41 4.7 24.4 1.0 C A:LEU20 4.9 14.3 1.0

Cobalt binding site 2 out of 4 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 Cobalt with other atoms in the Co 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:Co101 b:28.2 occ:1.00 CO A:NCO101 0.0 28.2 1.0 N6 A:NCO101 1.9 23.7 1.0 N1 A:NCO101 2.0 29.7 1.0 N3 A:NCO101 2.2 15.2 1.0 N5 A:NCO101 2.3 23.6 1.0 N4 A:NCO101 2.3 18.7 1.0 N2 A:NCO101 2.4 33.3 1.0 OE2 A:GLU44 4.0 19.4 1.0 O B:LEU20 4.0 13.8 1.0 O B:HOH244 4.2 28.5 1.0 OD2 A:ASP42 4.3 22.3 1.0 OE1 B:GLU51 4.4 25.7 1.0 O A:HOH217 4.4 21.1 1.0 O A:HOH211 4.5 46.4 1.0 OE1 A:GLU44 4.6 23.3 1.0 CD A:GLU44 4.7 19.6 1.0 O A:HOH203 4.7 17.3 1.0 CG A:ASP42 4.8 20.4 1.0

Cobalt binding site 3 out of 4 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 Cobalt with other atoms in the Co 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 A:Co103 b:30.2 occ:1.00 CO A:NCO103 0.0 30.2 1.0 N4 A:NCO103 1.8 9.4 1.0 N1 A:NCO103 2.0 21.7 1.0 N2 A:NCO103 2.1 21.4 1.0 N6 A:NCO103 2.2 11.0 1.0 N5 A:NCO103 2.4 29.7 1.0 N3 A:NCO103 2.7 18.5 1.0 O A:MET27 3.7 19.5 1.0 O A:HOH218 4.4 27.1 1.0 O A:HOH241 4.8 27.1 1.0 OD1 A:ASP29 4.8 37.9 1.0 C A:MET27 4.9 18.9 1.0

Cobalt binding site 4 out of 4 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 Cobalt with other atoms in the Co 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:Co104 b:28.7 occ:1.00 CO A:NCO104 0.0 28.7 1.0 N1 A:NCO104 2.0 30.5 1.0 N4 A:NCO104 2.0 24.4 1.0 N2 A:NCO104 2.2 18.1 1.0 N5 A:NCO104 2.3 21.7 1.0 N6 A:NCO104 2.4 32.2 1.0 N3 A:NCO104 2.5 18.6 1.0 O A:CYS56 3.6 17.4 1.0 OG A:SER59 3.9 22.6 1.0 O A:GLU54 4.2 20.6 1.0 C A:CYS56 4.8 17.1 1.0 C A:GLU54 4.9 19.6 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