6N4M: Nitrogenase iron protein 1

IDS-oxidized ADP-bound form of the nitrogenase Fe-protein from A. vinelandii. Determined by X-ray diffraction at 1.58 Å resolution. Released 13 Feb 2019.

Method: X-ray diffraction
Resolution: 1.58 Å
Organism: Azotobacter vinelandii
Chains: 1
Atoms: 2,287
Mol. weight: 32.22 kDa
Ligands: SF4, MG, ADP
Released: 13 Feb 2019

Explore 6N4M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N4M contains 15 α-helices and 9 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
α-helix	15-28	14
β-strand	33-38	6	1
α-helix	46-49	4
α-helix	57-64	8
α-helix	67-69	3
α-helix	72-75	4
β-strand	77-78	2	1
α-helix	80-82	3
β-strand	84-87	4	1
α-helix	91-92	2
α-helix	100-111	12
β-strand	121-126	6	1
α-helix	133-140	8
β-strand	146-151	6	1
α-helix	155-170	16
β-strand	178-185	8	1
α-helix	192-203	12
β-strand	207-211	5	1
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	1
α-helix	261-270	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitrogenase iron protein 1	A	protein	289	Azotobacter vinelandii	P00459 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6N4M_1 Nitrogenase iron protein 1 (chains A)
AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEM
AAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLD
FVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLG
GLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEY
RALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0States of the Nitrogenase Fe-Protein. Wenke, B.B., Spatzal, T., Rees, D.C. Angew Chem Int Ed Engl (2019) 58:3894-3897. DOI 10.1002/anie.201813966 · PubMed

Other PDB entries of the same protein (UniProt P00459 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6N4L 1.13 Å, Dithionite-reduced ADP-bound form of the nitrogenase Fe-protein from A. vinelandii
7TPW 1.18 Å, Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii
7TPO 1.35 Å, Selenium-incorporated nitrogenase Fe-protein (Av2-Se) from A. vinelandii (1 mM KSeCN)
7TPX 1.35 Å, Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii
7TPN 1.38 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN)
7TNE 1.39 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN)
7TQF 1.45 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (22 mM KSeCN)
7TQI 1.47 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN)
7TPY 1.48 Å, Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (nucleotide control)
7TQJ 1.48 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (1 mM KSeCN)
7TQK 1.48 Å, Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (1 mM KSeCN)
7TPV 1.49 Å, Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (5mM KSeCN Soaked)

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