1N2C: Nitrogenase molybdenum-iron protein

Nitrogenase complex from azotobacter vinelandii stabilized by ADP-tetrafluoroaluminate. Determined by X-ray diffraction at 3.0 Å resolution. Released 12 Nov 1997.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Azotobacter vinelandii
Chains: 8
Atoms: 24,426
Mol. weight: 361.25 kDa
Ligands: HCA, CFM, CA, 1CL
Released: 12 Nov 1997

Explore 1N2C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N2C contains 184 α-helices and 112 β-strands across 8 chains. 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: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	17-19	3
α-helix	22-29	8
β-strand	32-34	3	1
α-helix	51-53	3
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	2
α-helix	88-92	5
β-strand	98	1	3
β-strand	104	1	4
β-strand	108	1	4
β-strand	114-115	2	2
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	2
α-helix	154-159	6
α-helix	163-174	12
β-strand	178-181	4	2
α-helix	191-205	15
α-helix	207-210	4
β-strand	222-226	5	5
β-strand	231	1	3
α-helix	234-244	11
β-strand	248-253	6	5
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	5
α-helix	276-290	15
β-strand	294-296	3	5
α-helix	302-313	12
α-helix	318-346	29
β-strand	350-353	4	1
β-strand	355	1	1
α-helix	359-369	11
β-strand	373-379	7	1
α-helix	384-391	8
α-helix	395	1
β-strand	399-402	4	1
α-helix	406-416	11
β-strand	420-423	4	1
α-helix	425-434	10
β-strand	438-440	3	1
α-helix	444-446	3
α-helix	452-467	16
α-helix	470-475	6

Chain B: 35 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-14	4
α-helix	18-27	10
α-helix	28-32	5
α-helix	34-36	3
α-helix	37-47	11
α-helix	50-57	8
β-strand	63-64	2	2
α-helix	71-79	9
β-strand	82	1	6
β-strand	85-90	6	7
α-helix	93-103	11
α-helix	104-108	5
β-strand	114-115	2	7
α-helix	120-125	6
α-helix	128-142	15
β-strand	146-151	6	7
α-helix	153-157	5
α-helix	162-171	10
β-strand	183	1	7
α-helix	193-207	15
α-helix	211-214	4
β-strand	224-227	4	8
α-helix	234-247	14
β-strand	251-253	3	8
α-helix	260-262	3
β-strand	276	1	6
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	8
α-helix	295-297	3
α-helix	299-304	6
α-helix	305-309	5
α-helix	321-336	16
α-helix	342-362	21
β-strand	366-370	5	9
α-helix	373-386	14
β-strand	389-395	7	9
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	9
α-helix	427-436	10
β-strand	441-444	4	9
α-helix	446-448	3
α-helix	449-458	10
α-helix	460-462	3
β-strand	466-468	3	9
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chain C: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	17-19	3
α-helix	22-29	8
β-strand	32-34	3	10
α-helix	51-53	3
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	11
α-helix	88-92	5
β-strand	98	1	12
β-strand	104	1	13
β-strand	108	1	13
β-strand	114-115	2	11
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	11
α-helix	154-159	6
α-helix	163-174	12
β-strand	178-181	4	11
α-helix	191-205	15
α-helix	207-210	4
β-strand	222-226	5	14
β-strand	231	1	12
α-helix	234-244	11
β-strand	248-253	6	14
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	14
α-helix	276-290	15
β-strand	294-296	3	14
α-helix	302-313	12
α-helix	318-346	29
β-strand	350-353	4	10
β-strand	355	1	10
α-helix	359-362	4
α-helix	364-369	6
β-strand	373-379	7	10
α-helix	384-391	8
α-helix	395	1
β-strand	399-402	4	10
α-helix	406-416	11
β-strand	420-423	4	10
α-helix	425-433	9
β-strand	438-440	3	10
α-helix	444-446	3
α-helix	452-467	16
α-helix	470-475	6

Chain D: 34 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-14	4
α-helix	18-27	10
α-helix	28-32	5
α-helix	34-36	3
α-helix	37-47	11
α-helix	50-57	8
β-strand	63-64	2	11
α-helix	71-79	9
β-strand	82	1	15
β-strand	85-90	6	16
α-helix	93-107	15
β-strand	114-115	2	16
α-helix	120-125	6
α-helix	128-142	15
β-strand	146-151	6	16
α-helix	153-157	5
α-helix	162-171	10
β-strand	183	1	16
α-helix	193-207	15
α-helix	211-214	4
β-strand	224-227	4	17
α-helix	234-247	14
β-strand	251-253	3	17
α-helix	260-262	3
β-strand	276	1	15
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	17
α-helix	295-297	3
α-helix	299-304	6
α-helix	305-309	5
α-helix	321-336	16
α-helix	342-362	21
β-strand	366-370	5	18
α-helix	373-386	14
β-strand	389-395	7	18
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	18
α-helix	427-436	10
β-strand	441-444	4	18
α-helix	446-448	3
α-helix	449-458	10
α-helix	460-462	3
β-strand	466-468	3	18
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chains E and H: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	19
α-helix	15-28	14
β-strand	33-38	6	19
α-helix	46-49	4
α-helix	57-63	7
α-helix	67-69	3
α-helix	72-75	4
β-strand	77-78	2	19
α-helix	80-82	3
β-strand	84-87	4	19
α-helix	91-92	2
β-strand	97	1	20
α-helix	98-111	14
β-strand	121-126	6	19
β-strand	132	1	21
α-helix	133-139	7
β-strand	146-151	6	19
α-helix	155-174	20
β-strand	178-185	8	19
α-helix	192-203	12
β-strand	207-211	5	19
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	19
α-helix	261-271	11

Chains F and G: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	22
α-helix	15-28	14
β-strand	33-38	6	22
α-helix	46-49	4
α-helix	57-63	7
α-helix	67-69	3
α-helix	72-75	4
β-strand	77-78	2	22
α-helix	80-82	3
β-strand	84-87	4	22
α-helix	91-92	2
β-strand	97	1	21
α-helix	98-111	14
β-strand	121-126	6	22
β-strand	132	1	20
α-helix	134-139	6
β-strand	146-151	6	22
α-helix	155-174	20
β-strand	178-185	8	22
α-helix	192-203	12
β-strand	207-211	5	22
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	22
α-helix	261-271	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitrogenase molybdenum-iron protein	A, C	protein	491	Azotobacter vinelandii	P07328 (AlphaFold model)
Nitrogenase molybdenum-iron protein	B, D	protein	522	Azotobacter vinelandii	P07329 (AlphaFold model)
Nitrogenase iron protein	E, F, G, H	protein	289	Azotobacter vinelandii	P00459 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1N2C_1 NITROGENASE MOLYBDENUM-IRON PROTEIN (chains A, C)
TGMSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRG
CAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEK
DIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPV
RCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRIL
LEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFG
PTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPR
HVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLI
GSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWEA
SEGAEKVAASA

Sequence of entity 2 (B, D), FASTA

>1N2C_2 NITROGENASE MOLYBDENUM-IRON PROTEIN (chains B, D)
SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREA
LTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTED
AAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPV
PFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIK
RMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKT
KKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTW
LHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATV
YIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHR
STTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

Sequence of entity 3 (E, F, G, H), FASTA

>1N2C_3 NITROGENASE IRON PROTEIN (chains E, F, G, H)
AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEM
AAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLD
FVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLG
GLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEY
RALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV

Ligands and cofactors

ID	Name	Formula	Copies
HCA	3-hydroxy-3-carboxy-adipic acid	C7 H10 O7	2
CFM	FE-mo-S cluster	Fe7 Mo S9	2
CA	Calcium ion	Ca	2
1CL	FE(8)-S(7) cluster, oxidized	Fe8 S7	2
MG	Magnesium ion	Mg	4
ALF	Tetrafluoroaluminate ion	Al F4	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Schindelin, H., Kisker, C., Schlessman, J.L. et al. Nature (1997) 387:370-376. DOI 10.1038/387370a0 · PubMed

Other PDB entries of the same protein (UniProt P07328 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U7Q 1.0 Å, A. vinelandii nitrogenase MoFe protein at atomic resolution
1M1N 1.16 Å, Nitrogenase MoFe protein from Azotobacter vinelandii
7JRF 1.33 Å, Co-co-bound nitrogenase mofe-protein from a. Vinelandii
6O7M 1.4 Å, Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the indigo carmine oxidized…
4TKU 1.43 Å, Reactivated Nitrogenase MoFe-protein from A. vinelandii
4TKV 1.5 Å, CO-bound Nitrogenase MoFe-protein from A. vinelandii
5BVH 1.53 Å, CO-bound form of Selenium incorporated nitrogenase MoFe-protein (Av1-Se-CO) from A.…
8P8G 1.55 Å, Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G
5BVG 1.6 Å, Selenium incorporated nitrogenase MoFe-protein (Av1-Se2B) from A. vinelandii
6OP3 1.6 Å, Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low…
7MCI 1.65 Å, MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor
6BBL 1.68 Å, Crystal structure of the a-96Gln MoFe protein variant in the presence of the substrate…

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