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Iron in PDB 3pni: Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin

Protein crystallography data

The structure of Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin, PDB code: 3pni was solved by M.N.Loevgreen, 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) 35.70 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.400, 49.800, 51.230, 90.00, 90.00, 90.00
R / Rfree (%) 27.9 / 31.8

Other elements in 3pni:

The structure of Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin also contains other interesting chemical elements:

Cobalt (Co) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin (pdb code 3pni). 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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin, PDB code: 3pni:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3pni

Go back to Iron Binding Sites List in 3pni
Iron binding site 1 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe70

b:32.4
occ:1.00
 FE1 A:F3S70 0.0 32.4 1.0
S3 A:F3S70 2.1 37.6 1.0
S1 A:F3S70 2.2 31.7 1.0
SG A:CYS11 2.2 33.8 1.0
S2 A:F3S70 2.2 32.9 1.0
FE3 A:F3S70 2.5 35.0 1.0
FE4 A:F3S70 2.6 32.0 1.0
CB A:CYS11 3.1 37.8 1.0
CA A:CYS11 3.8 38.4 1.0
S4 A:F3S70 3.8 33.2 1.0
N A:ILE12 4.0 39.3 1.0
CB A:ALA33 4.1 32.7 1.0
N A:GLY13 4.3 39.3 1.0
C A:CYS11 4.4 39.1 1.0
N A:ALA33 4.4 32.9 1.0
SG A:CYS56 4.4 32.7 1.0
SG A:CYS17 4.6 40.1 0.9
CG1 A:VAL6 4.8 44.0 1.0
N A:CYS14 4.8 39.0 1.0
CA A:GLY13 4.9 39.1 1.0
CA A:ALA33 4.9 33.0 1.0

Iron binding site 2 out of 6 in 3pni

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Iron binding site 2 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe70

b:35.0
occ:1.00
 FE3 A:F3S70 0.0 35.0 1.0
S3 A:F3S70 2.1 37.6 1.0
SG A:CYS17 2.2 40.1 0.9
S1 A:F3S70 2.2 31.7 1.0
S4 A:F3S70 2.2 33.2 1.0
FE1 A:F3S70 2.5 32.4 1.0
FE4 A:F3S70 2.5 32.0 1.0
S2 A:F3S70 3.5 32.9 1.0
CB A:CYS17 3.5 40.6 0.9
CB A:ALA33 3.5 32.7 1.0
N A:CYS17 4.3 40.7 0.9
SG A:CYS11 4.4 33.8 1.0
N A:ALA15 4.4 39.5 1.0
CA A:CYS17 4.6 40.6 0.9
SG A:CYS56 4.6 32.7 1.0
CA A:ALA15 4.7 39.6 1.0
CD1 A:ILE61 4.7 32.2 1.0
CA A:ALA33 4.8 33.0 1.0
CB A:CYS56 4.9 34.5 1.0
N A:ILE16 4.9 40.4 1.0
N A:ALA33 5.0 32.9 1.0

Iron binding site 3 out of 6 in 3pni

Go back to Iron Binding Sites List in 3pni
Iron binding site 3 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe70

b:32.0
occ:1.00
 FE4 A:F3S70 0.0 32.0 1.0
S3 A:F3S70 2.1 37.6 1.0
S2 A:F3S70 2.2 32.9 1.0
SG A:CYS56 2.2 32.7 1.0
S4 A:F3S70 2.2 33.2 1.0
FE3 A:F3S70 2.5 35.0 1.0
FE1 A:F3S70 2.6 32.4 1.0
CB A:CYS56 3.1 34.5 1.0
S1 A:F3S70 3.6 31.7 1.0
CA A:CYS56 4.1 34.3 1.0
CD A:PRO57 4.4 34.2 1.0
SG A:CYS17 4.5 40.1 0.9
SG A:CYS11 4.7 33.8 1.0
C A:CYS56 4.7 34.4 1.0
CD1 A:ILE61 4.7 32.2 1.0
CG2 A:VAL58 4.8 34.5 1.0
N A:PRO57 4.8 34.2 1.0
CB A:CYS14 4.9 40.1 1.0
CG1 A:ILE61 5.0 34.5 1.0

Iron binding site 4 out of 6 in 3pni

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Iron binding site 4 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe70

b:27.3
occ:1.00
 FE1 B:F3S70 0.0 27.3 1.0
S3 B:F3S70 2.1 29.8 1.0
SG B:CYS11 2.1 33.7 1.0
S2 B:F3S70 2.2 26.8 1.0
S1 B:F3S70 2.2 27.1 1.0
FE3 B:F3S70 2.5 27.0 1.0
FE4 B:F3S70 2.5 28.1 1.0
CB B:CYS11 3.2 37.9 1.0
S4 B:F3S70 3.8 26.3 1.0
CA B:CYS11 3.8 38.4 1.0
CB B:ALA33 4.0 32.5 1.0
N B:ILE12 4.1 39.3 1.0
N B:GLY13 4.1 39.3 1.0
N B:ALA33 4.2 32.8 1.0
C B:CYS11 4.4 39.0 1.0
SG B:CYS17 4.5 39.9 0.9
SG B:CYS56 4.6 32.4 1.0
CA B:GLY13 4.6 39.1 1.0
CA B:ALA33 4.7 32.8 1.0
N B:CYS14 4.8 38.9 1.0
CG1 B:VAL6 4.9 44.0 1.0

Iron binding site 5 out of 6 in 3pni

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Iron binding site 5 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe70

b:27.0
occ:1.00
 FE3 B:F3S70 0.0 27.0 1.0
S3 B:F3S70 2.1 29.8 1.0
SG B:CYS17 2.1 39.9 0.9
S4 B:F3S70 2.2 26.3 1.0
S1 B:F3S70 2.2 27.1 1.0
FE4 B:F3S70 2.5 28.1 1.0
FE1 B:F3S70 2.5 27.3 1.0
CB B:ALA33 3.5 32.5 1.0
CB B:CYS17 3.5 40.7 0.9
S2 B:F3S70 3.6 26.8 1.0
N B:CYS17 4.2 40.7 0.9
N B:ALA15 4.4 39.3 1.0
SG B:CYS11 4.4 33.7 1.0
CA B:ALA15 4.5 39.4 1.0
CA B:CYS17 4.5 40.7 0.9
SG B:CYS56 4.7 32.4 1.0
CD1 B:ILE61 4.7 32.3 1.0
CA B:ALA33 4.7 32.8 1.0
N B:ILE16 4.8 40.3 1.0
N B:ALA33 4.9 32.8 1.0
C B:ALA15 4.9 39.9 1.0
CB B:CYS56 5.0 34.4 1.0

Iron binding site 6 out of 6 in 3pni

Go back to Iron Binding Sites List in 3pni
Iron binding site 6 out of 6 in the Crystal Structure of D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin


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 D14C [3FE-4S] Pyrococcus Furiosus Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe70

b:28.1
occ:1.00
 FE4 B:F3S70 0.0 28.1 1.0
S3 B:F3S70 2.1 29.8 1.0
S4 B:F3S70 2.2 26.3 1.0
S2 B:F3S70 2.2 26.8 1.0
SG B:CYS56 2.3 32.4 1.0
FE3 B:F3S70 2.5 27.0 1.0
FE1 B:F3S70 2.5 27.3 1.0
CB B:CYS56 3.3 34.4 1.0
S1 B:F3S70 3.5 27.1 1.0
SG B:CYS14 4.1 37.7 0.5
CA B:CYS56 4.2 34.2 1.0
SG B:CYS17 4.5 39.9 0.9
CD B:PRO57 4.6 34.0 1.0
SG B:CYS11 4.6 33.7 1.0
CD1 B:ILE61 4.8 32.3 1.0
C B:CYS56 4.8 34.2 1.0
CG2 B:VAL58 4.9 34.5 1.0
N B:PRO57 5.0 34.1 1.0

Reference:

M.N.Lovgreen, M.Martic, M.S.Windahl, H.E.Christensen, P.Harris. Crystal Structures of the All Cysteinyl Coordinated D14C Variant of Pyrococcus Furiosus Ferredoxin: [4FE-4S] <-> [3FE-4S] Cluster Conversion J.Biol.Inorg.Chem. V. 16 763 2011.
ISSN: ISSN 0949-8257
PubMed: 21484348
DOI: 10.1007/S00775-011-0778-7
Page generated: Sun Aug 4 18:07:10 2024

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