Iron in PDB 8rb8: Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added (pdb code 8rb8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added, PDB code: 8rb8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:47.0 occ:1.00 FE1 A:FES200 0.0 47.0 1.0 S1 A:FES200 2.2 36.3 1.0 S2 A:FES200 2.2 62.5 1.0 SG E:CYS122 2.3 69.5 1.0 SG A:CYS25 2.3 53.0 1.0 FE2 A:FES200 2.7 36.3 1.0 CB A:CYS25 3.0 25.3 1.0 CB E:CYS122 3.3 64.5 1.0 N E:CYS122 3.9 57.1 1.0 N E:ALA37 4.1 49.1 1.0 N A:CYS25 4.2 28.5 1.0 CA A:CYS25 4.2 26.6 1.0 CA E:CYS122 4.2 62.3 1.0 SG A:CYS113 4.3 46.3 1.0 SG E:CYS39 4.4 58.1 1.0 CA E:ALA37 4.6 40.5 1.0 N E:LEU38 4.7 47.3 1.0 O E:THR120 4.7 78.8 1.0 CD A:PRO26 4.9 34.4 1.0

Iron binding site 2 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:36.3 occ:1.00 FE2 A:FES200 0.0 36.3 1.0 S2 A:FES200 2.2 62.5 1.0 S1 A:FES200 2.2 36.3 1.0 SG A:CYS113 2.3 46.3 1.0 SG E:CYS39 2.3 58.1 1.0 FE1 A:FES200 2.7 47.0 1.0 CB A:CYS113 3.3 30.9 1.0 CB E:CYS39 3.6 41.1 1.0 O A:ASN112 3.7 51.1 1.0 SG A:CYS25 4.3 53.0 1.0 C A:ASN112 4.4 42.9 1.0 N A:GLY23 4.4 27.3 1.0 SG E:CYS122 4.4 69.5 1.0 N E:CYS39 4.5 40.8 1.0 CA A:CYS113 4.5 34.0 1.0 N A:LEU24 4.6 26.6 1.0 O E:THR120 4.6 78.8 1.0 CA A:GLY23 4.6 23.7 1.0 N A:CYS113 4.7 37.9 1.0 CA E:CYS39 4.7 32.8 1.0 N A:CYS25 4.9 28.5 1.0 CB A:CYS25 5.0 25.3 1.0

Iron binding site 3 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:32.8 occ:1.00 FE1 C:SF4501 0.0 32.8 1.0 SG C:CYS376 2.3 68.3 1.0 S3 C:SF4501 2.3 43.5 1.0 S4 C:SF4501 2.3 57.8 1.0 S2 C:SF4501 2.3 58.1 1.0 FE2 C:SF4501 2.7 59.3 1.0 FE3 C:SF4501 2.7 56.4 1.0 FE4 C:SF4501 2.7 49.8 1.0 CB C:CYS376 3.5 39.4 1.0 S1 C:SF4501 3.9 60.6 1.0 N C:CYS376 4.2 42.4 1.0 SG C:CYS419 4.4 37.4 1.0 CB C:LEU387 4.4 28.4 1.0 CA C:CYS376 4.4 40.1 1.0 CD2 C:LEU387 4.7 36.5 1.0 CD1 C:LEU425 4.7 20.1 1.0 SG C:CYS373 4.7 37.5 1.0 SG C:CYS370 4.8 52.1 1.0 OG C:SER375 4.8 50.2 1.0 CA C:LEU387 5.0 32.2 1.0 N C:SER375 5.0 40.2 1.0 N C:LEU387 5.0 37.5 1.0

Iron binding site 4 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:59.3 occ:1.00 FE2 C:SF4501 0.0 59.3 1.0 SG C:CYS419 2.3 37.4 1.0 S3 C:SF4501 2.3 43.5 1.0 S4 C:SF4501 2.3 57.8 1.0 S1 C:SF4501 2.3 60.6 1.0 FE1 C:SF4501 2.7 32.8 1.0 FE3 C:SF4501 2.7 56.4 1.0 FE4 C:SF4501 2.7 49.8 1.0 CB C:CYS419 3.8 17.0 1.0 S2 C:SF4501 3.9 58.1 1.0 SG C:CYS376 4.1 68.3 1.0 OG C:SER421 4.1 32.2 1.0 CA C:CYS419 4.2 16.8 1.0 O C:SER421 4.2 42.2 1.0 CD C:PRO420 4.3 34.9 1.0 CD1 C:ILE423 4.7 28.8 1.0 N C:PRO420 4.7 32.1 1.0 SG C:CYS373 4.7 37.5 1.0 SG C:CYS370 4.7 52.1 1.0 C C:CYS419 4.7 28.4 1.0 CD1 C:LEU425 4.8 20.1 1.0 N C:SER421 4.9 17.8 1.0

Iron binding site 5 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added 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 52.1 1.0 S4 C:SF4501 2.3 57.8 1.0 S1 C:SF4501 2.3 60.6 1.0 S2 C:SF4501 2.3 58.1 1.0 FE4 C:SF4501 2.7 49.8 1.0 FE2 C:SF4501 2.7 59.3 1.0 FE1 C:SF4501 2.7 32.8 1.0 CB C:CYS370 3.4 36.5 1.0 N C:ARG372 3.7 37.1 1.0 S3 C:SF4501 3.9 43.5 1.0 CA C:CYS370 4.0 33.4 1.0 N C:ILE371 4.1 27.2 1.0 CA C:ARG372 4.1 34.2 1.0 C C:CYS370 4.4 34.0 1.0 CB C:LEU387 4.5 28.4 1.0 N C:CYS373 4.5 36.9 1.0 C C:ILE371 4.8 35.9 1.0 C C:ARG372 4.8 39.4 1.0 SG C:CYS373 4.8 37.5 1.0 SG C:CYS419 4.9 37.4 1.0 SG C:CYS376 5.0 68.3 1.0

Iron binding site 6 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:49.8 occ:1.00 FE4 C:SF4501 0.0 49.8 1.0 SG C:CYS373 2.3 37.5 1.0 S3 C:SF4501 2.3 43.5 1.0 S1 C:SF4501 2.3 60.6 1.0 S2 C:SF4501 2.3 58.1 1.0 FE3 C:SF4501 2.7 56.4 1.0 FE2 C:SF4501 2.7 59.3 1.0 FE1 C:SF4501 2.7 32.8 1.0 N C:CYS373 3.5 36.9 1.0 CB C:CYS373 3.7 37.0 1.0 OG C:SER375 3.7 50.2 1.0 S4 C:SF4501 3.9 57.8 1.0 CD C:PRO420 4.0 34.9 1.0 N C:ALA374 4.0 30.2 1.0 CA C:CYS373 4.0 36.8 1.0 C C:CYS373 4.3 33.9 1.0 N C:SER375 4.3 40.2 1.0 SG C:CYS376 4.4 68.3 1.0 N C:ARG372 4.5 37.1 1.0 C C:ARG372 4.5 39.4 1.0 SG C:CYS419 4.6 37.4 1.0 CA C:ARG372 4.7 34.2 1.0 CG C:PRO420 4.7 30.8 1.0 CG1 C:ILE371 4.7 31.5 1.0 SG C:CYS370 4.8 52.1 1.0 CB C:SER375 4.9 35.0 1.0 CA C:ALA374 4.9 35.4 1.0 N C:CYS376 5.0 42.4 1.0

Iron binding site 7 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:56.2 occ:1.00 FE1 C:SF4502 0.0 56.2 1.0 SG C:CYS409 2.3 39.4 1.0 S2 C:SF4502 2.3 51.0 1.0 S4 C:SF4502 2.3 55.9 1.0 S3 C:SF4502 2.3 57.2 1.0 FE3 C:SF4502 2.7 35.6 1.0 FE2 C:SF4502 2.7 60.9 1.0 FE4 C:SF4502 2.7 36.0 1.0 CB C:CYS409 3.3 33.3 1.0 CA C:CYS409 3.6 32.5 1.0 N C:ILE410 3.8 26.5 1.0 N C:LEU411 3.9 32.8 1.0 S1 C:SF4502 3.9 52.7 1.0 C C:CYS409 4.2 42.6 1.0 CA C:LEU411 4.5 26.0 1.0 CD1 C:LEU384 4.6 33.0 1.0 N C:CYS412 4.7 28.0 1.0 C C:ILE410 4.8 34.3 1.0 SG C:CYS415 4.8 64.1 1.0 CD2 C:PHE429 4.8 32.2 1.0 CA C:ILE410 4.8 27.1 1.0 SG C:CYS412 4.9 39.6 1.0 SG C:CYS380 4.9 60.0 1.0 CE2 C:PHE429 4.9 28.9 1.0 CG1 C:ILE410 4.9 30.6 1.0 N C:CYS409 5.0 35.9 1.0

Iron binding site 8 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:60.9 occ:1.00 FE2 C:SF4502 0.0 60.9 1.0 SG C:CYS412 2.3 39.6 1.0 S1 C:SF4502 2.3 52.7 1.0 S3 C:SF4502 2.3 57.2 1.0 S4 C:SF4502 2.3 55.9 1.0 FE3 C:SF4502 2.7 35.6 1.0 FE1 C:SF4502 2.7 56.2 1.0 FE4 C:SF4502 2.7 36.0 1.0 N C:CYS412 3.6 28.0 1.0 CB C:CYS412 3.6 29.9 1.0 S2 C:SF4502 3.9 51.0 1.0 CA C:CYS412 4.0 21.0 1.0 N C:GLY413 4.1 25.1 1.0 CD C:PRO381 4.1 37.1 1.0 N C:CYS414 4.3 35.0 1.0 CG1 C:ILE410 4.4 30.6 1.0 C C:CYS412 4.4 26.1 1.0 N C:LEU411 4.5 32.8 1.0 C C:LEU411 4.6 30.7 1.0 CB C:CYS414 4.7 31.7 1.0 SG C:CYS409 4.7 39.4 1.0 SG C:CYS380 4.7 60.0 1.0 CA C:LEU411 4.8 26.0 1.0 SG C:CYS415 4.8 64.1 1.0 CG C:PRO381 4.9 31.1 1.0 N C:ILE410 5.0 26.5 1.0

Iron binding site 9 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:35.6 occ:1.00 FE3 C:SF4502 0.0 35.6 1.0 SG C:CYS415 2.2 64.1 1.0 S4 C:SF4502 2.3 55.9 1.0 S1 C:SF4502 2.3 52.7 1.0 S2 C:SF4502 2.3 51.0 1.0 FE1 C:SF4502 2.7 56.2 1.0 FE4 C:SF4502 2.7 36.0 1.0 FE2 C:SF4502 2.7 60.9 1.0 CB C:CYS415 3.6 42.4 1.0 S3 C:SF4502 3.9 57.2 1.0 N C:CYS415 4.0 39.5 1.0 CE2 C:PHE429 4.1 28.9 1.0 CA C:CYS415 4.3 28.8 1.0 SG C:CYS409 4.5 39.4 1.0 CD2 C:PHE429 4.6 32.2 1.0 CG C:PRO386 4.6 28.3 1.0 SG C:CYS380 4.6 60.0 1.0 SG C:CYS412 4.7 39.6 1.0 N C:CYS414 4.8 35.0 1.0 C C:CYS414 4.9 39.0 1.0 CB C:PRO386 5.0 24.6 1.0

Iron binding site 10 out of 18 in the Cryo-Em Structure of the Nadh:Ferredoxin Oxidoreductase Rnf From Azotobacter Vinelandii, Purified with 2-Me/Tcep, Nadh Added


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, Purified with 2-Me/Tcep, Nadh Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:36.0 occ:1.00 FE4 C:SF4502 0.0 36.0 1.0 SG C:CYS380 2.3 60.0 1.0 S2 C:SF4502 2.3 51.0 1.0 S1 C:SF4502 2.3 52.7 1.0 S3 C:SF4502 2.3 57.2 1.0 FE3 C:SF4502 2.7 35.6 1.0 FE2 C:SF4502 2.7 60.9 1.0 FE1 C:SF4502 2.7 56.2 1.0 CB C:CYS380 3.4 30.3 1.0 S4 C:SF4502 3.9 55.9 1.0 CA C:CYS380 4.0 23.5 1.0 CD C:PRO381 4.1 37.1 1.0 CD1 C:LEU384 4.1 33.0 1.0 N C:PRO381 4.5 28.5 1.0 SG C:CYS415 4.5 64.1 1.0 C C:CYS380 4.5 38.3 1.0 N C:MET382 4.6 27.7 1.0 CG C:LEU384 4.7 31.5 1.0 SG C:CYS412 4.7 39.6 1.0 CB C:MET382 4.7 25.6 1.0 CG C:MET382 4.7 32.1 1.0 CB C:LEU384 4.9 35.3 1.0 SG C:CYS409 4.9 39.4 1.0

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