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

Protein crystallography data

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

Other elements in 2z8q:

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

Iron (Fe) 8 atoms

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 5 in 2z8q

Go back to Cobalt Binding Sites List in 2z8q
Cobalt binding site 1 out of 5 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co102

b:7.3
occ:1.00
CO A:NCO102 0.0 7.3 1.0
N3 A:NCO102 2.0 12.2 1.0
N6 A:NCO102 2.0 9.1 1.0
N4 A:NCO102 2.0 15.2 1.0
N1 A:NCO102 2.0 6.7 1.0
N2 A:NCO102 2.0 9.8 1.0
N5 A:NCO102 2.0 7.4 1.0
O A:GLU54 3.6 6.6 0.5
O A:CYS56 3.8 2.5 1.0
O A:GLU54 3.8 9.0 0.5
OG A:SER59 3.8 8.5 1.0
O A:HOH259 3.9 22.4 1.0
O A:HOH233 4.3 26.9 1.0
O A:HOH265 4.3 25.7 1.0
O B:HOH230 4.6 24.9 1.0
C A:GLU54 4.7 5.1 0.5
C A:GLU54 4.8 6.7 0.5
C A:CYS56 4.9 2.7 1.0

Cobalt binding site 2 out of 5 in 2z8q

Go back to Cobalt Binding Sites List in 2z8q
Cobalt binding site 2 out of 5 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:5.0
occ:0.50
CO A:NCO103 0.0 5.0 0.5
CO A:NCO103 1.2 9.1 0.5
N5 A:NCO103 2.0 13.3 1.0
N3 A:NCO103 2.0 15.8 1.0
N4 A:NCO103 2.1 12.0 1.0
N2 A:NCO103 2.4 20.7 1.0
N6 A:NCO103 2.5 27.3 1.0
N1 A:NCO103 2.6 18.7 1.0
O A:HOH293 3.5 17.0 1.0
O A:ILE12 3.9 5.9 1.0
O A:HOH254 4.1 19.8 1.0
O A:HOH236 4.4 20.5 1.0

Cobalt binding site 3 out of 5 in 2z8q

Go back to Cobalt Binding Sites List in 2z8q
Cobalt binding site 3 out of 5 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:9.1
occ:0.50
CO A:NCO103 0.0 9.1 0.5
CO A:NCO103 1.2 5.0 0.5
N2 A:NCO103 1.9 20.7 1.0
N4 A:NCO103 1.9 12.0 1.0
N3 A:NCO103 2.2 15.8 1.0
O A:HOH293 2.6 17.0 1.0
N5 A:NCO103 2.6 13.3 1.0
N6 A:NCO103 3.4 27.3 1.0
N1 A:NCO103 3.6 18.7 1.0
O A:ILE12 3.7 5.9 1.0
O A:HOH231 4.0 27.6 1.0
O A:HOH254 4.6 19.8 1.0
O A:GLY13 4.8 5.9 1.0
C A:ILE12 5.0 4.9 1.0

Cobalt binding site 4 out of 5 in 2z8q

Go back to Cobalt Binding Sites List in 2z8q
Cobalt binding site 4 out of 5 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co102

b:14.1
occ:1.00
CO B:NCO102 0.0 14.1 1.0
N5 B:NCO102 2.0 15.7 1.0
N3 B:NCO102 2.0 14.8 1.0
N2 B:NCO102 2.0 15.4 1.0
N1 B:NCO102 2.0 11.1 1.0
N4 B:NCO102 2.0 14.0 1.0
N6 B:NCO102 2.0 13.2 1.0
O B:HOH223 3.7 22.2 1.0
OE2 B:GLU44 3.8 19.5 1.0
OE1 B:GLU43 4.2 31.0 1.0
OE1 B:GLU44 4.3 15.6 1.0
OD2 B:ASP42 4.4 17.3 1.0
CD B:GLU44 4.5 16.4 1.0
CG B:ASP42 4.6 17.4 1.0
CB B:ASP42 4.8 15.1 1.0
O B:HOH210 4.9 13.7 1.0

Cobalt binding site 5 out of 5 in 2z8q

Go back to Cobalt Binding Sites List in 2z8q
Cobalt binding site 5 out of 5 in the Ferredoxin From Pyrococcus Furiosus, D14C Variant


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Ferredoxin From Pyrococcus Furiosus, D14C Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co103

b:16.5
occ:0.50
CO B:NCO103 0.0 16.5 0.5
N1 B:NCO103 2.0 18.3 0.5
N2 B:NCO103 2.0 18.3 0.5
N3 B:NCO103 2.0 16.5 0.5
N5 B:NCO103 2.0 20.5 0.5
N6 B:NCO103 2.0 19.5 0.5
N4 B:NCO103 2.0 19.5 0.5
O B:GLU54 3.9 16.2 1.0
O B:HOH207 4.0 11.6 1.0
OG A:SER19 4.4 8.4 0.5
O A:SER19 4.4 3.3 0.5
O A:SER19 4.9 3.2 0.5
O B:HOH218 4.9 19.1 1.0
O B:HOH250 5.0 23.4 1.0

Reference:

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.
Page generated: Sun Jul 13 18:39:26 2025

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