4WZA: Nitrogenase molybdenum-iron protein alpha chain

Asymmetric Nucleotide Binding in the Nitrogenase Complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 31 Dec 2014.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Azotobacter vinelandii
Chains: 8
Atoms: 26,654
Mol. weight: 353.03 kDa
Ligands: HCA, ICS, CLF, FE
Released: 31 Dec 2014

Explore 4WZA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WZA contains 180 α-helices and 120 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, 23 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	22-29	8
β-strand	32-34	3	1
α-helix	42-44	3
α-helix	51-53	3
β-strand	58	1	2
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	3
α-helix	87-91	5
β-strand	98	1	4
β-strand	104	1	5
β-strand	108	1	5
β-strand	114-115	2	3
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	3
α-helix	154-159	6
α-helix	163-174	12
β-strand	178-181	4	3
α-helix	191-205	15
β-strand	222-228	7	6
β-strand	231	1	4
α-helix	236-244	9
β-strand	248-254	7	6
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	6
α-helix	276-290	15
β-strand	294-296	3	6
β-strand	300	1	7
α-helix	302-313	12
α-helix	318-346	29
β-strand	350-353	4	1
β-strand	355	1	1
α-helix	359-362	4
α-helix	364-369	6
β-strand	373-379	7	1
α-helix	384-391	8
α-helix	395	1
β-strand	399-402	4	1
β-strand	405	1	2
α-helix	406-416	11
β-strand	420-423	4	1
α-helix	425-433	9
β-strand	438-440	3	1
α-helix	444-446	3
β-strand	451	1	7
α-helix	452-467	16
α-helix	470-473	4

Chain B: 32 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	18-27	10
α-helix	28-32	5
α-helix	34-36	3
α-helix	37-46	10
α-helix	50-57	8
β-strand	63-64	2	3
α-helix	71-80	10
β-strand	82	1	8
β-strand	85-90	6	9
α-helix	93-107	15
β-strand	114-115	2	9
α-helix	120-125	6
α-helix	128-142	15
β-strand	146-151	6	9
α-helix	153-157	5
α-helix	162-171	10
β-strand	183	1	9
α-helix	193-209	17
α-helix	210-215	6
β-strand	224-227	4	10
α-helix	234-247	14
β-strand	251-253	3	10
β-strand	276	1	8
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	10
α-helix	295-297	3
α-helix	299-307	9
β-strand	320	1	11
α-helix	321-336	16
α-helix	338-341	4
α-helix	342-362	21
β-strand	366-370	5	12
α-helix	373-385	13
β-strand	389-395	7	12
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	12
α-helix	427-436	10
β-strand	441-444	4	12
α-helix	446-448	3
α-helix	449-458	10
α-helix	460-462	3
β-strand	466-468	3	12
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chain C: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	22-29	8
β-strand	32-34	3	13
α-helix	42-44	3
α-helix	51-53	3
α-helix	63-64	2
α-helix	65-72	8
β-strand	79-83	5	14
α-helix	87-91	5
β-strand	98	1	15
β-strand	104	1	16
β-strand	108	1	16
β-strand	114-115	2	14
α-helix	120-125	6
α-helix	128-141	14
β-strand	148-152	5	14
α-helix	154-159	6
α-helix	163-174	12
β-strand	178-181	4	14
α-helix	191-205	15
α-helix	207-210	4
β-strand	222-228	7	17
β-strand	231	1	15
α-helix	236-244	9
β-strand	248-254	7	17
α-helix	259-264	6
α-helix	265-267	3
β-strand	270-273	4	17
α-helix	276-290	15
β-strand	294-296	3	17
β-strand	300	1	18
α-helix	301-313	13
α-helix	318-346	29
β-strand	350-353	4	13
β-strand	355	1	13
α-helix	359-362	4
α-helix	364-369	6
β-strand	373-379	7	13
α-helix	384-390	7
α-helix	391-393	3
β-strand	399-402	4	13
α-helix	406-416	11
β-strand	420-423	4	13
α-helix	425-433	9
β-strand	438-440	3	13
α-helix	444-446	3
β-strand	451	1	18
α-helix	452-467	16
α-helix	470-474	5

Chain D: 30 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	19
α-helix	11-14	4
α-helix	18-31	14
α-helix	34-36	3
α-helix	37-46	10
α-helix	50-56	7
β-strand	63-64	2	14
α-helix	71-80	10
β-strand	82	1	20
β-strand	85-90	6	21
α-helix	93-107	15
β-strand	114-115	2	21
α-helix	120-125	6
α-helix	128-142	15
β-strand	146-151	6	21
α-helix	153-157	5
α-helix	162-171	10
β-strand	183	1	21
α-helix	193-209	17
α-helix	210-215	6
β-strand	224-227	4	22
α-helix	234-247	14
β-strand	251-253	3	22
β-strand	276	1	20
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	22
α-helix	295-297	3
α-helix	299-307	9
α-helix	321-336	16
α-helix	338-341	4
α-helix	342-362	21
β-strand	366-370	5	23
α-helix	373-385	13
β-strand	389-395	7	23
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	23
α-helix	427-436	10
β-strand	441-444	4	23
α-helix	448-458	11
α-helix	460-462	3
β-strand	466-468	3	23
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chain E: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	24
α-helix	15-28	14
β-strand	33-38	6	24
α-helix	46-49	4
α-helix	57-64	8
α-helix	67-69	3
α-helix	72-74	3
β-strand	77-78	2	24
α-helix	80-82	3
β-strand	84-87	4	24
α-helix	91-92	2
β-strand	97	1	25
α-helix	98-111	14
β-strand	121-126	6	24
β-strand	132	1	26
α-helix	133-139	7
β-strand	146-151	6	24
α-helix	155-174	20
β-strand	178-185	8	24
α-helix	192-203	12
β-strand	207-211	5	24
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	24
α-helix	261-270	10

Chain F: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3-9	7	27
α-helix	15-28	14
β-strand	33-38	6	27
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	27
α-helix	80-82	3
β-strand	84-87	4	27
α-helix	91-92	2
β-strand	97	1	26
α-helix	98-111	14
β-strand	121-126	6	27
β-strand	132	1	25
α-helix	133-139	7
β-strand	146-151	6	27
α-helix	155-172	18
β-strand	178-185	8	27
α-helix	192-203	12
β-strand	207-211	5	27
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	27
α-helix	261-269	9

Chain G: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	28
α-helix	15-28	14
β-strand	33-38	6	28
α-helix	46-49	4
α-helix	54-56	3
α-helix	57-64	8
α-helix	67-69	3
α-helix	72-74	3
β-strand	77-78	2	28
α-helix	80-82	3
β-strand	84-87	4	28
α-helix	91-92	2
β-strand	97	1	29
α-helix	98-111	14
β-strand	121-126	6	28
β-strand	132	1	30
α-helix	133-139	7
β-strand	146-151	6	28
α-helix	155-174	20
β-strand	178-185	8	28
α-helix	192-203	12
β-strand	207-211	5	28
α-helix	216-221	6
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	28
α-helix	261-270	10

Chain H: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	31
α-helix	15-28	14
β-strand	33-38	6	31
α-helix	46-49	4
α-helix	57-64	8
α-helix	67-69	3
α-helix	72-74	3
β-strand	77-78	2	31
α-helix	80-82	3
β-strand	84-87	4	31
α-helix	91-92	2
β-strand	97	1	30
α-helix	98-111	14
β-strand	121-126	6	31
β-strand	132	1	29
α-helix	133-139	7
β-strand	146-151	6	31
α-helix	155-172	18
β-strand	178-185	8	31
α-helix	192-203	12
β-strand	207-211	5	31
α-helix	212-213	2
α-helix	216-222	7
α-helix	227-230	4
α-helix	235-249	15
β-strand	254	1	31
α-helix	261-269	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nitrogenase molybdenum-iron protein alpha chain	A, C	protein	477	Azotobacter vinelandii	P07328 (AlphaFold model)
Nitrogenase molybdenum-iron protein beta chain	B, D	protein	522	Azotobacter vinelandii	P07329 (AlphaFold model)
Nitrogenase iron protein 1	E, F, G, H	protein	276	Azotobacter vinelandii	P00459 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4WZA_1 Nitrogenase molybdenum-iron protein alpha chain (chains A, C)
MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCA
YAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDI
VFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRC
EGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLE
EMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPT
KTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHV
IGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGS
GIKEKFIFQKMGIPFRQMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE

Sequence of entity 2 (B, D), FASTA

>4WZA_2 Nitrogenase molybdenum-iron protein beta chain (chains B, D)
SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREA
LTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTED
AAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPV
PFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIK
RMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKT
KKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTW
LHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATV
YIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHR
STTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

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

>4WZA_3 Nitrogenase iron protein 1 (chains E, F, G, H)
AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEM
AAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLD
FVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLG
GLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEY
RALARKVVDNKLLVIPNPITMDELEELLMEFGIMEV

Ligands and cofactors

ID	Name	Formula	Copies
HCA	3-hydroxy-3-carboxy-adipic acid	C7 H10 O7	2
ICS	iron-sulfur-molybdenum cluster with interstitial carbon	C Fe7 Mo S9	2
CLF	FE(8)-S(7) cluster	Fe8 S7	2
FE	FE (III) ion	Fe	2
SF4	Iron/sulfur cluster	Fe4 S4	2
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	2

Primary citation

Structural evidence for asymmetrical nucleotide interactions in nitrogenase. Tezcan, F.A., Kaiser, J.T., Howard, J.B. et al. J Am Chem Soc (2015) 137:146-149. DOI 10.1021/ja511945e · 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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