6OP3: Nitrogenase molybdenum-iron protein alpha chain

Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Azotobacter vinelandii
Chains: 4
Atoms: 18,377
Mol. weight: 231.34 kDa
Ligands: CA, MG, CLF, SE
Released: 14 Aug 2019

Explore 6OP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OP3 contains 117 α-helices and 76 β-strands across 4 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, 21 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	87-92	6
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	155-158	4
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
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	364-368	5
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
α-helix	452-467	16
α-helix	470-473	4

Chain B: 32 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	7	1	7
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	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	122-125	4
α-helix	128-142	15
β-strand	146-151	6	9
α-helix	153-158	6
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	234-246	13
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
α-helix	321-336	16
α-helix	338-341	4
α-helix	342-362	21
β-strand	366-370	5	11
α-helix	373-385	13
β-strand	389-395	7	11
α-helix	400-411	12
α-helix	414-416	3
β-strand	420-423	4	11
α-helix	427-436	10
β-strand	441-444	4	11
α-helix	446-448	3
α-helix	449-458	10
α-helix	460-462	3
β-strand	466-468	3	11
α-helix	479-481	3
α-helix	486-508	23
α-helix	516-518	3

Chain C: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	22-29	8
β-strand	32-34	3	12
α-helix	42-44	3
α-helix	51-53	3
β-strand	58	1	13
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	155-158	4
α-helix	163-174	12
β-strand	178-181	4	14
α-helix	191-205	15
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
α-helix	302-313	12
α-helix	318-346	29
β-strand	350-353	4	12
β-strand	355	1	12
α-helix	359-362	4
α-helix	364-368	5
β-strand	373-379	7	12
α-helix	384-391	8
α-helix	395	1
β-strand	399-402	4	12
β-strand	405	1	13
α-helix	406-416	11
β-strand	420-423	4	12
α-helix	425-433	9
β-strand	438-440	3	12
α-helix	444-446	3
α-helix	452-467	16
α-helix	470-473	4

Chain D: 31 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	18
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	14
α-helix	71-80	10
β-strand	82	1	19
β-strand	85-90	6	20
α-helix	93-107	15
β-strand	114-115	2	20
α-helix	122-125	4
α-helix	128-142	15
β-strand	146-151	6	20
α-helix	153-158	6
α-helix	162-171	10
β-strand	183	1	20
α-helix	193-209	17
α-helix	210-215	6
β-strand	224-227	4	21
α-helix	234-246	13
β-strand	251-253	3	21
β-strand	276	1	19
α-helix	278-283	6
α-helix	284-286	3
β-strand	289-292	4	21
α-helix	295-297	3
α-helix	299-307	9
β-strand	320	1	22
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

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)

Sequence of entity 1 (A, C), FASTA

>6OP3_1 Nitrogenase molybdenum-iron protein alpha chain (chains A, C)
MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCA
YAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDI
VFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRC
EGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLE
EMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPT
KTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHV
IGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGS
GIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE

Sequence of entity 2 (B, D), FASTA

>6OP3_2 Nitrogenase molybdenum-iron protein beta chain (chains B, D)
SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREA
LTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTED
AAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPV
PFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIK
RMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKT
KKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTW
LHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATV
YIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHR
STTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	2
CLF	FE(8)-S(7) cluster	Fe8 S7	2
SE	Selenium atom	Se	2
ICS	iron-sulfur-molybdenum cluster with interstitial carbon	C Fe7 Mo S9	2
HCA	3-hydroxy-3-carboxy-adipic acid	C7 H10 O7	2

Water and common crystallization additives (IMD) are not listed.

Primary citation

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. Henthorn, J.T., Arias, R.J., Koroidov, S. et al. J Am Chem Soc (2019) 141:13676-13688. DOI 10.1021/jacs.9b06988 · 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
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…
6O7P 1.7 Å, Nitrogenase MoFeP mutant F99Y from Azotobacter vinelandii in the dithionite reduced state

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