SMTL ID : 8dfc.1

CryoEM structure of the 1:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

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

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

HCA.2: 8 residues within 4Å: Chain A: A.65, V.70, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:G.95, B:R.105 Salt bridges: A:H.442, A:H.442 HCA.6: 7 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.5 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain C Water bridges: D:R.105, C:R.97, C:G.424, C:G.424, C:H.442 Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Salt bridges: C:H.442, C:H.442

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

CLF.3: 20 residues within 4Å: Chain A: C.62, Y.64, P.85, V.86, G.87, C.88, Y.91, E.153, 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: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, A:C.62, A:C.88, A:C.88, A:C.154 Salt bridges: A:E.153 CLF.7: 19 residues within 4Å: Chain C: C.62, Y.64, P.85, V.86, C.88, Y.91, E.153, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, C:C.62, C:C.88, C:C.88, C:C.154 Salt bridges: C:E.153

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

FE.4: 5 residues within 4Å: Chain B: D.353, D.357 Chain C: K.433 Chain D: R.108, E.109 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:R.108, B:D.353, B:D.357, H2O.3, H2O.13 FE.8: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:R.108, D:D.353, D:D.357, H2O.13, H2O.15

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

SF4.9: 14 residues within 4Å: Chain C: L.158, I.159 Chain D: V.157, I.158 Chain E: C.98, A.99, G.100, V.132, 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 ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)(Non-covalent)

ADP.10: 22 residues within 4Å: Chain E: G.12, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237 Chain F: K.11, E.155, M.156, M.157 Ligands: ALF.11, MG.12 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.13, E:I.14, E:K.16, E:S.17, E:T.18, E:N.186, E:P.213, E:D.215, E:E.222, E:Q.237, F:M.156 Salt bridges: E:K.16, F:K.11, F:K.11 ADP.14: 23 residues within 4Å: Chain E: K.11, E.155, M.157 Chain F: G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.44, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237, Y.241 Ligands: MG.13, ALF.15 18 PLIP interactions: 15 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:N.186, F:P.213, F:R.214, F:D.215, F:E.222, F:Q.237, F:Y.241, E:M.157 Salt bridges: F:K.16, E:K.11, E:K.11

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.11: 10 residues within 4Å: Chain E: G.12, G.13, K.16, K.42, D.44, G.129 Chain F: K.11, D.130 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) ALF.15: 9 residues within 4Å: Chain E: K.11 Chain F: G.12, G.13, K.16, D.40, D.44, G.129 Ligands: MG.13, ADP.14 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 6 residues within 4Å: Chain E: S.17, D.44, S.45, D.126 Ligands: ADP.10, ALF.11 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain F: S.17, D.44 Ligands: ADP.14, ALF.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warmack, R.A. et al., Anaerobic cryoEM protocols for air-sensitive nitrogenase proteins. Nat Protoc (2024)

Release Date

2023-06-28

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
Nitrogenase iron protein 1: 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 1

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