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Iron in PDB 6n2n: Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus

Protein crystallography data

The structure of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus, PDB code: 6n2n was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 98.15 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.282, 123.161, 162.487, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.5

Other elements in 6n2n:

The structure of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus (pdb code 6n2n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus, PDB code: 6n2n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6n2n

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Iron binding site 1 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:25.6
occ:1.00
FE1 B:SF4401 0.0 25.6 1.0
SG B:CYS209 2.3 24.8 1.0
S4 B:SF4401 2.3 24.4 1.0
S2 B:SF4401 2.3 25.9 1.0
S3 B:SF4401 2.3 27.1 1.0
FE3 B:SF4401 2.7 22.7 1.0
FE2 B:SF4401 2.7 27.2 1.0
FE4 B:SF4401 2.8 23.6 1.0
CB B:CYS209 3.3 24.4 1.0
CA B:CYS209 3.8 27.2 1.0
S1 B:SF4401 3.9 23.1 1.0
O B:HOH604 4.4 25.1 1.0
C B:CYS209 4.4 27.5 1.0
CD2 B:PHE212 4.4 25.3 1.0
CB B:THR211 4.5 27.4 1.0
CA B:GLY134 4.5 22.8 1.0
OG1 B:THR211 4.7 25.9 1.0
SG B:CYS29 4.8 24.9 1.0
N B:THR211 4.8 27.7 1.0
ND2 B:ASN130 4.8 22.4 1.0
SG B:CYS60 4.8 24.8 1.0
SG B:CYS26 4.9 25.1 1.0
N B:PRO210 4.9 27.4 1.0
O B:CYS209 4.9 24.5 1.0
CE2 B:PHE212 5.0 26.8 1.0

Iron binding site 2 out of 8 in 6n2n

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Iron binding site 2 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:27.2
occ:1.00
FE2 B:SF4401 0.0 27.2 1.0
SG B:CYS29 2.3 24.9 1.0
S3 B:SF4401 2.3 27.1 1.0
S1 B:SF4401 2.3 23.1 1.0
S4 B:SF4401 2.3 24.4 1.0
FE4 B:SF4401 2.7 23.6 1.0
FE3 B:SF4401 2.7 22.7 1.0
FE1 B:SF4401 2.7 25.6 1.0
CB B:CYS29 3.1 25.9 1.0
O B:HOH604 3.8 25.1 1.0
S2 B:SF4401 3.9 25.9 1.0
CA B:CYS29 4.2 28.4 1.0
CD2 B:HIS31 4.3 26.2 1.0
N B:CYS26 4.5 28.9 1.0
NE2 B:HIS31 4.6 25.1 1.0
CB B:CYS26 4.6 27.1 1.0
SG B:CYS26 4.7 25.1 1.0
CB B:TRP25 4.7 27.3 1.0
CB B:CYS60 4.7 23.7 1.0
SG B:CYS209 4.7 24.8 1.0
SG B:CYS60 4.7 24.8 1.0
CD1 B:TRP25 4.8 26.0 1.0
O B:GLN208 4.8 26.5 1.0
CG B:HIS31 4.8 26.0 1.0
CG B:TRP25 4.9 26.8 1.0
CA B:CYS209 4.9 27.2 1.0
CB B:CYS209 4.9 24.4 1.0

Iron binding site 3 out of 8 in 6n2n

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Iron binding site 3 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:22.7
occ:1.00
FE3 B:SF4401 0.0 22.7 1.0
S2 B:SF4401 2.3 25.9 1.0
S4 B:SF4401 2.3 24.4 1.0
S1 B:SF4401 2.3 23.1 1.0
SG B:CYS60 2.3 24.8 1.0
FE4 B:SF4401 2.7 23.6 1.0
FE1 B:SF4401 2.7 25.6 1.0
FE2 B:SF4401 2.7 27.2 1.0
CB B:CYS60 3.1 23.7 1.0
S3 B:SF4401 3.9 27.1 1.0
O B:HOH528 3.9 28.6 1.0
CA B:GLY134 4.4 22.8 1.0
C B:GLY134 4.5 25.2 1.0
CA B:CYS60 4.6 23.2 1.0
CD1 A:ILE46 4.6 28.1 1.0
SG B:CYS29 4.8 24.9 1.0
N B:LEU135 4.8 23.7 1.0
O B:GLY134 4.8 26.5 1.0
SG B:CYS26 4.8 25.1 1.0
SG B:CYS209 4.8 24.8 1.0
O3B B:TPP402 4.9 23.5 1.0
CD1 B:TRP25 5.0 26.0 1.0

Iron binding site 4 out of 8 in 6n2n

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Iron binding site 4 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:23.6
occ:1.00
FE4 B:SF4401 0.0 23.6 1.0
S1 B:SF4401 2.3 23.1 1.0
S3 B:SF4401 2.3 27.1 1.0
SG B:CYS26 2.3 25.1 1.0
S2 B:SF4401 2.3 25.9 1.0
FE2 B:SF4401 2.7 27.2 1.0
FE3 B:SF4401 2.7 22.7 1.0
FE1 B:SF4401 2.8 25.6 1.0
CB B:CYS26 3.1 27.1 1.0
OG1 B:THR211 3.7 25.9 1.0
N B:CYS26 3.8 28.9 1.0
S4 B:SF4401 3.9 24.4 1.0
CA B:CYS26 4.1 30.2 1.0
CB B:THR211 4.2 27.4 1.0
CG2 A:ILE46 4.4 28.2 1.0
O B:HOH610 4.5 30.9 1.0
CB B:CYS29 4.7 25.9 1.0
SG B:CYS29 4.8 24.9 1.0
SG B:CYS209 4.8 24.8 1.0
SG B:CYS60 4.8 24.8 1.0
CB A:ILE46 4.9 29.7 1.0
O B:HOH528 5.0 28.6 1.0
CG2 B:THR211 5.0 28.3 1.0

Iron binding site 5 out of 8 in 6n2n

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Iron binding site 5 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:22.8
occ:1.00
FE1 D:SF4401 0.0 22.8 1.0
S3 D:SF4401 2.3 21.8 1.0
SG D:CYS209 2.3 22.6 1.0
S4 D:SF4401 2.3 23.8 1.0
S2 D:SF4401 2.3 23.9 1.0
FE2 D:SF4401 2.7 22.6 1.0
FE3 D:SF4401 2.7 20.6 1.0
FE4 D:SF4401 2.8 22.6 1.0
CB D:CYS209 3.3 21.8 1.0
CA D:CYS209 3.8 24.6 1.0
S1 D:SF4401 3.9 22.8 1.0
O D:HOH571 4.3 22.0 1.0
C D:CYS209 4.4 23.0 1.0
CB D:THR211 4.4 23.4 1.0
CA D:GLY134 4.5 18.7 1.0
CD2 D:PHE212 4.5 21.2 1.0
OG1 D:THR211 4.7 28.5 1.0
N D:THR211 4.7 22.9 1.0
SG D:CYS29 4.7 23.4 1.0
ND2 D:ASN130 4.8 22.1 1.0
SG D:CYS60 4.8 21.1 1.0
SG D:CYS26 4.8 24.9 1.0
O D:CYS209 4.9 22.9 1.0
N D:PRO210 4.9 24.4 1.0

Iron binding site 6 out of 8 in 6n2n

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Iron binding site 6 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:22.6
occ:1.00
FE2 D:SF4401 0.0 22.6 1.0
SG D:CYS29 2.3 23.4 1.0
S4 D:SF4401 2.3 23.8 1.0
S1 D:SF4401 2.3 22.8 1.0
S3 D:SF4401 2.3 21.8 1.0
FE4 D:SF4401 2.7 22.6 1.0
FE3 D:SF4401 2.7 20.6 1.0
FE1 D:SF4401 2.7 22.8 1.0
CB D:CYS29 3.1 23.4 1.0
O D:HOH571 3.8 22.0 1.0
S2 D:SF4401 3.9 23.9 1.0
CA D:CYS29 4.2 23.9 1.0
CD2 D:HIS31 4.2 22.4 1.0
N D:CYS26 4.5 27.0 1.0
NE2 D:HIS31 4.6 24.1 1.0
CB D:CYS26 4.6 26.2 1.0
CB D:TRP25 4.7 24.7 1.0
CB D:CYS60 4.7 21.5 1.0
SG D:CYS26 4.7 24.9 1.0
SG D:CYS60 4.7 21.1 1.0
CG D:HIS31 4.7 22.5 1.0
SG D:CYS209 4.8 22.6 1.0
CD1 D:TRP25 4.8 25.9 1.0
CG D:TRP25 4.8 23.9 1.0
O D:GLN208 4.9 24.1 1.0
CA D:CYS209 4.9 24.6 1.0
CB D:CYS209 4.9 21.8 1.0

Iron binding site 7 out of 8 in 6n2n

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Iron binding site 7 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:20.6
occ:1.00
FE3 D:SF4401 0.0 20.6 1.0
S4 D:SF4401 2.3 23.8 1.0
S1 D:SF4401 2.3 22.8 1.0
S2 D:SF4401 2.3 23.9 1.0
SG D:CYS60 2.3 21.1 1.0
FE4 D:SF4401 2.7 22.6 1.0
FE2 D:SF4401 2.7 22.6 1.0
FE1 D:SF4401 2.7 22.8 1.0
CB D:CYS60 3.1 21.5 1.0
S3 D:SF4401 3.9 21.8 1.0
O D:HOH659 3.9 25.2 1.0
CA D:GLY134 4.4 18.7 1.0
C D:GLY134 4.5 21.6 1.0
CA D:CYS60 4.5 23.3 1.0
CD1 C:ILE46 4.7 28.5 1.0
N D:LEU135 4.7 19.6 1.0
O D:GLY134 4.8 22.0 1.0
SG D:CYS26 4.8 24.9 1.0
SG D:CYS29 4.8 23.4 1.0
O2B D:TPP402 4.8 19.1 1.0
SG D:CYS209 4.8 22.6 1.0
CD1 D:TRP25 5.0 25.9 1.0

Iron binding site 8 out of 8 in 6n2n

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Iron binding site 8 out of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:22.6
occ:1.00
FE4 D:SF4401 0.0 22.6 1.0
S1 D:SF4401 2.3 22.8 1.0
S2 D:SF4401 2.3 23.9 1.0
S3 D:SF4401 2.3 21.8 1.0
SG D:CYS26 2.3 24.9 1.0
FE3 D:SF4401 2.7 20.6 1.0
FE2 D:SF4401 2.7 22.6 1.0
FE1 D:SF4401 2.8 22.8 1.0
CB D:CYS26 3.1 26.2 1.0
OG1 D:THR211 3.7 28.5 1.0
N D:CYS26 3.8 27.0 1.0
S4 D:SF4401 3.9 23.8 1.0
CA D:CYS26 4.0 26.4 1.0
CB D:THR211 4.1 23.4 1.0
O D:HOH597 4.4 30.0 1.0
CG2 C:ILE46 4.4 27.1 1.0
CB D:CYS29 4.7 23.4 1.0
SG D:CYS29 4.8 23.4 1.0
CB C:ILE46 4.8 30.4 1.0
SG D:CYS209 4.8 22.6 1.0
SG D:CYS60 4.8 21.1 1.0
CG2 D:THR211 4.9 27.5 1.0
C D:TRP25 5.0 28.4 1.0
O D:HOH659 5.0 25.2 1.0

Reference:

P.Y.Chen, B.Li, C.L.Drennan, S.J.Elliott. A Reverse Tca Cycle 2-Oxoacid:Ferredoxin Oxidoreductase That Makes C-C Bonds From CO2. Joule V. 3 595 2019.
ISSN: ESSN 2542-4351
PubMed: 31080943
DOI: 10.1016/J.JOULE.2018.12.006
Page generated: Wed Aug 6 10:06:14 2025

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