SMTL ID : 7ut8.1

CryoEM structure of Azotobacter vinelandii nitrogenase complex (1:1 FeP:MoFeP, ATP-bound) during catalytic N2 reduction

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.1: 9 residues within 4Å: Chain A: A.65, G.95, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425, B:S.101 Salt bridges: A:K.426, A:H.442 HCA.5: 7 residues within 4Å: Chain C: G.95, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.191, C:I.425 Salt bridges: C:K.426, C:H.442

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.2: 15 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.6: 14 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.5 1 PLIP interactions: 1 interactions with chain C, Metal complexes: C:C.275

2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.3: 18 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, C.154, G.185 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153 CLF.8: 18 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D, Metal complexes: C:C.62, C:C.88, C:C.88, C:C.154, D:C.70, D:C.95, D:C.95, D:C.153

2 x FE: FE (III) ION(Non-covalent)

FE.4: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357 FE.7: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Metal complexes: B:R.108, B:E.109, D:D.357

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.9: 11 residues within 4Å: Chain A: L.158 Chain B: V.157 Chain E: C.98, A.99, G.100, C.133 Chain F: C.98, A.99, G.100, V.132, C.133 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, Metal complexes: F:C.98, F:C.133, E:C.98, E:C.133

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain E: S.17, D.40, D.44 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.12: 3 residues within 4Å: Chain F: S.17, D.40 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.11: 24 residues within 4Å: Chain E: K.11, G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, K.42, G.129, N.186, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237 Chain F: K.11, D.130, E.155, M.157 Ligands: MG.10 26 PLIP interactions: 20 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:S.17, E:T.18, E:T.18, E:G.129, E:N.186, E:P.213, E:R.214, E:D.215, E:Q.219, E:E.222, E:Q.237, F:D.130, F:E.155, F:M.157 Salt bridges: E:K.16, E:K.16, E:K.42, E:K.42, F:K.11, F:K.11, F:K.11 pi-Cation interactions: E:R.214 ATP.13: 22 residues within 4Å: Chain E: K.11, M.157 Chain F: K.11, G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, K.42, G.129, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:K.11, F:G.13, F:I.14, F:G.15, F:K.16, F:S.17, F:T.18, F:T.18, F:G.129, F:N.186, F:P.213, F:D.215, F:E.222 Salt bridges: F:K.16, F:K.16, F:K.42, E:K.11, E:K.11, E:K.11 pi-Cation interactions: F:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutledge, H.L. et al., Structures of the nitrogenase complex prepared under catalytic turnover conditions. Science (2022)

Release Date

2022-08-17

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
Nitrogenase iron protein gamma chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Nitrogenase iron protein gamma chain

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