Iron in PDB 8rbm: Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized (pdb code 8rbm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized, PDB code: 8rbm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 8rbm

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Iron binding site 1 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:82.0
occ:1.00
 FE1 A:FES201 0.0 82.0 1.0
S1 A:FES201 2.2 79.9 1.0
S2 A:FES201 2.2 92.0 1.0
SG A:CYS25 2.3 81.1 1.0
SG E:CYS122 2.3 49.7 1.0
FE2 A:FES201 2.7 84.4 1.0
CB A:CYS25 3.0 63.2 1.0
CB E:CYS122 3.5 45.0 1.0
N E:CYS122 4.1 43.2 1.0
N A:CYS25 4.2 64.7 1.0
SG A:CYS113 4.2 85.4 1.0
N E:ALA37 4.2 30.2 1.0
CA A:CYS25 4.2 62.4 1.0
CA E:CYS122 4.4 45.8 1.0
SG E:CYS39 4.4 29.8 1.0
O E:THR120 4.5 42.0 1.0
CA E:ALA37 4.6 16.0 1.0
N E:LEU38 4.7 13.6 1.0
CD A:PRO26 4.8 65.5 1.0

Iron binding site 2 out of 10 in 8rbm

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Iron binding site 2 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:84.4
occ:1.00
 FE2 A:FES201 0.0 84.4 1.0
S1 A:FES201 2.2 79.9 1.0
S2 A:FES201 2.2 92.0 1.0
SG E:CYS39 2.3 29.8 1.0
SG A:CYS113 2.3 85.4 1.0
FE1 A:FES201 2.7 82.0 1.0
CB A:CYS113 3.4 55.2 1.0
CB E:CYS39 3.7 14.4 1.0
O A:ASN112 3.8 85.8 1.0
SG A:CYS25 4.2 81.1 1.0
N E:CYS39 4.5 8.1 1.0
N A:GLY23 4.5 56.5 1.0
C A:ASN112 4.5 74.6 1.0
SG E:CYS122 4.6 49.7 1.0
O E:THR120 4.6 42.0 1.0
N A:LEU24 4.6 61.6 1.0
CA A:CYS113 4.6 58.6 1.0
CA E:CYS39 4.7 5.0 1.0
N A:CYS113 4.8 64.6 1.0
CA A:GLY23 4.8 54.9 1.0
N A:CYS25 4.9 64.7 1.0

Iron binding site 3 out of 10 in 8rbm

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Iron binding site 3 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:52.0
occ:1.00
 FE1 C:SF4501 0.0 52.0 1.0
SG C:CYS376 2.3 79.0 1.0
S3 C:SF4501 2.3 48.2 1.0
S4 C:SF4501 2.3 64.5 1.0
S2 C:SF4501 2.3 60.8 1.0
FE2 C:SF4501 2.7 59.8 1.0
FE3 C:SF4501 2.7 56.4 1.0
FE4 C:SF4501 2.7 60.9 1.0
CB C:CYS376 3.5 47.5 1.0
S1 C:SF4501 3.9 64.5 1.0
N C:CYS376 4.0 53.3 1.0
CA C:CYS376 4.4 51.9 1.0
CB C:LEU387 4.4 52.1 1.0
SG C:CYS419 4.4 62.3 1.0
OG C:SER375 4.5 51.4 1.0
CD1 C:LEU425 4.7 27.1 1.0
SG C:CYS373 4.7 57.5 1.0
SG C:CYS370 4.8 49.3 1.0
CD2 C:LEU387 4.9 51.5 1.0
N C:SER375 4.9 43.1 1.0
CA C:LEU387 5.0 43.8 1.0

Iron binding site 4 out of 10 in 8rbm

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Iron binding site 4 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:59.8
occ:1.00
 FE2 C:SF4501 0.0 59.8 1.0
SG C:CYS419 2.3 62.3 1.0
S3 C:SF4501 2.3 48.2 1.0
S4 C:SF4501 2.3 64.5 1.0
S1 C:SF4501 2.3 64.5 1.0
FE1 C:SF4501 2.7 52.0 1.0
FE4 C:SF4501 2.7 60.9 1.0
FE3 C:SF4501 2.7 56.4 1.0
CB C:CYS419 3.7 37.8 1.0
S2 C:SF4501 3.9 60.8 1.0
CA C:CYS419 4.0 30.0 1.0
OG C:SER421 4.0 23.7 1.0
SG C:CYS376 4.1 79.0 1.0
CD C:PRO420 4.2 44.1 1.0
O C:SER421 4.2 55.0 1.0
N C:PRO420 4.5 43.5 1.0
C C:CYS419 4.6 46.2 1.0
SG C:CYS373 4.7 57.5 1.0
SG C:CYS370 4.8 49.3 1.0
CD1 C:ILE423 4.8 42.8 1.0
N C:SER421 4.9 41.0 1.0
CD1 C:LEU425 4.9 27.1 1.0
OG C:SER375 5.0 51.4 1.0

Iron binding site 5 out of 10 in 8rbm

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Iron binding site 5 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:56.4
occ:1.00
 FE3 C:SF4501 0.0 56.4 1.0
SG C:CYS370 2.3 49.3 1.0
S4 C:SF4501 2.3 64.5 1.0
S2 C:SF4501 2.3 60.8 1.0
S1 C:SF4501 2.3 64.5 1.0
FE1 C:SF4501 2.7 52.0 1.0
FE4 C:SF4501 2.7 60.9 1.0
FE2 C:SF4501 2.7 59.8 1.0
CB C:CYS370 3.4 46.2 1.0
N C:ARG372 3.7 37.6 1.0
S3 C:SF4501 3.9 48.2 1.0
CA C:CYS370 3.9 39.0 1.0
N C:ILE371 4.1 34.1 1.0
CA C:ARG372 4.2 25.1 1.0
C C:CYS370 4.4 45.0 1.0
N C:CYS373 4.5 31.4 1.0
CB C:LEU387 4.6 52.1 1.0
C C:ILE371 4.8 38.1 1.0
SG C:CYS373 4.8 57.5 1.0
OG C:SER421 4.9 23.7 1.0
SG C:CYS419 4.9 62.3 1.0
C C:ARG372 4.9 29.2 1.0
SG C:CYS376 4.9 79.0 1.0

Iron binding site 6 out of 10 in 8rbm

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Iron binding site 6 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:60.9
occ:1.00
 FE4 C:SF4501 0.0 60.9 1.0
SG C:CYS373 2.3 57.5 1.0
S3 C:SF4501 2.3 48.2 1.0
S1 C:SF4501 2.3 64.5 1.0
S2 C:SF4501 2.3 60.8 1.0
FE2 C:SF4501 2.7 59.8 1.0
FE3 C:SF4501 2.7 56.4 1.0
FE1 C:SF4501 2.7 52.0 1.0
N C:CYS373 3.5 31.4 1.0
OG C:SER375 3.6 51.4 1.0
CB C:CYS373 3.6 42.7 1.0
S4 C:SF4501 3.9 64.5 1.0
CA C:CYS373 4.0 40.0 1.0
CD C:PRO420 4.0 44.1 1.0
N C:ALA374 4.0 42.1 1.0
N C:SER375 4.3 43.1 1.0
C C:CYS373 4.3 45.0 1.0
N C:ARG372 4.5 37.6 1.0
C C:ARG372 4.5 29.2 1.0
SG C:CYS376 4.6 79.0 1.0
CG1 C:ILE371 4.7 34.6 1.0
CG C:PRO420 4.7 39.1 1.0
CA C:ARG372 4.7 25.1 1.0
CB C:SER375 4.7 36.1 1.0
SG C:CYS419 4.8 62.3 1.0
SG C:CYS370 4.8 49.3 1.0
N C:CYS376 4.9 53.3 1.0
CA C:ALA374 5.0 37.0 1.0

Iron binding site 7 out of 10 in 8rbm

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Iron binding site 7 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:77.8
occ:1.00
 FE1 C:SF4502 0.0 77.8 1.0
SG C:CYS409 2.3 46.2 1.0
S2 C:SF4502 2.3 74.1 1.0
S4 C:SF4502 2.3 56.3 1.0
S3 C:SF4502 2.3 57.7 1.0
FE3 C:SF4502 2.7 50.0 1.0
FE2 C:SF4502 2.7 51.8 1.0
FE4 C:SF4502 2.7 55.4 1.0
CB C:CYS409 3.2 41.5 1.0
CA C:CYS409 3.6 44.3 1.0
N C:ILE410 3.7 39.4 1.0
S1 C:SF4502 3.9 54.9 1.0
N C:LEU411 3.9 50.5 1.0
C C:CYS409 4.1 49.3 1.0
CA C:LEU411 4.5 41.7 1.0
CD1 C:LEU384 4.5 46.0 1.0
N C:CYS412 4.8 51.0 1.0
CD2 C:PHE429 4.8 53.0 1.0
C C:ILE410 4.8 45.0 1.0
CA C:ILE410 4.8 27.5 1.0
SG C:CYS415 4.9 64.8 1.0
SG C:CYS412 4.9 51.6 1.0
SG C:CYS380 4.9 60.8 1.0
CE2 C:PHE429 4.9 46.9 1.0
N C:CYS409 4.9 46.1 1.0
CG1 C:ILE410 5.0 44.4 1.0

Iron binding site 8 out of 10 in 8rbm

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Iron binding site 8 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:51.8
occ:1.00
 FE2 C:SF4502 0.0 51.8 1.0
SG C:CYS412 2.3 51.6 1.0
S1 C:SF4502 2.3 54.9 1.0
S4 C:SF4502 2.3 56.3 1.0
S3 C:SF4502 2.3 57.7 1.0
FE3 C:SF4502 2.7 50.0 1.0
FE4 C:SF4502 2.7 55.4 1.0
FE1 C:SF4502 2.7 77.8 1.0
N C:CYS412 3.6 51.0 1.0
CB C:CYS412 3.6 39.0 1.0
S2 C:SF4502 3.9 74.1 1.0
CA C:CYS412 4.1 41.3 1.0
N C:GLY413 4.2 38.8 1.0
CD C:PRO381 4.2 51.4 1.0
CG1 C:ILE410 4.4 44.4 1.0
N C:CYS414 4.4 50.5 1.0
N C:LEU411 4.5 50.5 1.0
C C:CYS412 4.5 47.7 1.0
C C:LEU411 4.6 54.2 1.0
SG C:CYS409 4.7 46.2 1.0
SG C:CYS380 4.7 60.8 1.0
SG C:CYS415 4.7 64.8 1.0
CB C:CYS414 4.8 27.1 1.0
CA C:LEU411 4.8 41.7 1.0
N C:ILE410 4.9 39.4 1.0
CG C:PRO381 5.0 51.4 1.0

Iron binding site 9 out of 10 in 8rbm

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Iron binding site 9 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:50.0
occ:1.00
 FE3 C:SF4502 0.0 50.0 1.0
SG C:CYS415 2.2 64.8 1.0
S4 C:SF4502 2.3 56.3 1.0
S1 C:SF4502 2.3 54.9 1.0
S2 C:SF4502 2.3 74.1 1.0
FE1 C:SF4502 2.7 77.8 1.0
FE4 C:SF4502 2.7 55.4 1.0
FE2 C:SF4502 2.7 51.8 1.0
CB C:CYS415 3.7 51.4 1.0
S3 C:SF4502 3.9 57.7 1.0
CE2 C:PHE429 4.0 46.9 1.0
N C:CYS415 4.2 49.7 1.0
CG C:PRO386 4.4 33.9 1.0
CA C:CYS415 4.4 42.9 1.0
CD2 C:PHE429 4.5 53.0 1.0
SG C:CYS409 4.5 46.2 1.0
SG C:CYS380 4.6 60.8 1.0
SG C:CYS412 4.7 51.6 1.0
CB C:PRO386 4.8 38.2 1.0

Iron binding site 10 out of 10 in 8rbm

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Iron binding site 10 out of 10 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Ferricyanide Oxidized within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:55.4
occ:1.00
 FE4 C:SF4502 0.0 55.4 1.0
SG C:CYS380 2.3 60.8 1.0
S1 C:SF4502 2.3 54.9 1.0
S2 C:SF4502 2.3 74.1 1.0
S3 C:SF4502 2.3 57.7 1.0
FE3 C:SF4502 2.7 50.0 1.0
FE2 C:SF4502 2.7 51.8 1.0
FE1 C:SF4502 2.7 77.8 1.0
CB C:CYS380 3.4 36.3 1.0
S4 C:SF4502 3.9 56.3 1.0
CA C:CYS380 4.0 34.6 1.0
CD1 C:LEU384 4.1 46.0 1.0
CD C:PRO381 4.2 51.4 1.0
SG C:CYS415 4.5 64.8 1.0
N C:PRO381 4.6 45.7 1.0
C C:CYS380 4.6 47.2 1.0
CG C:LEU384 4.6 38.6 1.0
CG C:MET382 4.6 39.1 1.0
SG C:CYS412 4.7 51.6 1.0
N C:MET382 4.7 44.7 1.0
CB C:LEU384 4.7 42.6 1.0
CB C:MET382 4.8 40.0 1.0
CG C:PRO386 4.8 33.9 1.0
SG C:CYS409 4.9 46.2 1.0

Reference:

L.Zhang, O.Einsle. Architecture of the RNF1 Complex That Drives Biological Nitrogen Fixation. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38890433
DOI: 10.1038/S41589-024-01641-1
Page generated: Sat Aug 10 16:36:22 2024

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