SMTL ID : 8dfd.1

CryoEM structure of the 2:1 ADP-tetrafluoroaluminate stabilized nitrogenase complex from Azotobacter vinelandii

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-4-mer

Ligands

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

ICS.1: 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.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: 7 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.1 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:A.65, A:R.97, A:K.426, A:E.440, A:E.440, A:E.440, A:S.443, B:Y.98, B:R.105 Salt bridges: A:K.426, 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 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:R.97, C:K.426, C:E.440, C:E.440, C:E.440, C:S.443, D:R.105 Salt bridges: C:K.426, C:H.442, C:H.442

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

CLF.3: 19 residues within 4Å: Chain A: C.62, Y.64, P.85, 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, 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, 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: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:R.108, D:E.109, B:D.357, B:D.357, H2O.13 FE.8: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.353, D:D.357, D:D.357, B:E.109, H2O.43

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

SF4.9: 14 residues within 4Å: Chain A: L.158, I.159 Chain B: 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 E, 2 interactions with chain F, Metal complexes: E:C.98, E:C.133, F:C.98, F:C.133 SF4.19: 14 residues within 4Å: Chain C: L.158, I.159 Chain D: V.157, I.158 Chain G: C.98, A.99, G.100, V.132, C.133 Chain H: C.98, A.99, G.100, V.132, C.133 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, Metal complexes: G:C.98, G:C.133, H:C.98, H:C.133

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.10: 22 residues within 4Å: Chain E: K.11, 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, Y.241 Chain F: K.11, E.155, M.157 Ligands: ALF.11, MG.12 26 PLIP interactions: 23 interactions with chain E, 3 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:N.186, E:P.213, E:R.214, E:D.215, E:E.222, E:E.222, E:Q.237, E:Y.241, F:M.157 Water bridges: E:S.17, E:S.17, E:D.40, E:D.44, E:D.44, E:D.126 Salt bridges: E:K.16, F:K.11, F:K.11 pi-Cation interactions: E:R.214 ADP.13: 22 residues within 4Å: Chain E: K.11, E.155, M.157 Chain F: K.11, 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, Y.241 Ligands: ALF.14, MG.15 22 PLIP interactions: 18 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:G.13, F:I.14, F:G.15, 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:Q.219, F:E.222, F:Q.237, E:M.157 Water bridges: F:S.17, F:D.40, E:M.156 Salt bridges: F:K.16, E:K.11, E:K.11 pi-Cation interactions: F:R.214 ADP.16: 22 residues within 4Å: Chain G: K.11, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, V.218, Q.219, E.222, Q.237, Y.241 Chain H: K.11, E.155, M.156, M.157 Ligands: ALF.17, MG.18 24 PLIP interactions: 20 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:G.13, G:I.14, G:G.15, G:K.16, G:S.17, G:T.18, G:T.18, G:N.186, G:P.213, G:R.214, G:D.215, G:E.222, G:E.222, G:Q.237, G:Y.241, H:M.156, H:M.157 Water bridges: G:S.17, G:S.17, G:K.42 Salt bridges: G:K.16, H:K.11, H:K.11 pi-Cation interactions: G:R.214 ADP.20: 22 residues within 4Å: Chain G: K.11, E.155, M.157 Chain H: K.11, 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, Y.241 Ligands: ALF.21, MG.22 25 PLIP interactions: 20 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:G.13, H:I.14, H:G.15, H:G.15, H:K.16, H:S.17, H:T.18, H:N.186, H:P.213, H:R.214, H:D.215, H:Q.219, H:E.222, H:Q.237, G:M.157 Water bridges: H:S.17, H:S.17, H:D.40, H:V.127, G:K.11, G:K.11 Salt bridges: H:K.16, G:K.11, G:K.11 pi-Cation interactions: H:R.214

4 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.11: 11 residues within 4Å: Chain E: G.12, G.13, K.16, D.40, K.42, D.44, L.128, G.129 Chain F: K.11 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) ALF.14: 12 residues within 4Å: Chain E: K.11, G.12 Chain F: G.12, G.13, K.16, S.17, D.40, K.42, L.128, G.129 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP) ALF.17: 12 residues within 4Å: Chain G: G.12, G.13, K.16, D.40, K.42, D.44, V.127, L.128, G.129 Chain H: K.11 Ligands: ADP.16, MG.18 No protein-ligand interaction detected (PLIP) ALF.21: 12 residues within 4Å: Chain G: K.11, G.12 Chain H: G.12, G.13, K.16, S.17, D.40, K.42, L.128, G.129 Ligands: ADP.20, MG.22 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain E: S.17, D.126 Ligands: ADP.10, ALF.11 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.17, E:D.126, H2O.61, H2O.61, H2O.62 MG.15: 6 residues within 4Å: Chain F: S.17, S.45, D.126, V.127 Ligands: ADP.13, ALF.14 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.17, F:D.126, H2O.64, H2O.64, H2O.64 MG.18: 4 residues within 4Å: Chain G: S.17, D.126 Ligands: ADP.16, ALF.17 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:S.17, H2O.67, H2O.68, H2O.68 MG.22: 5 residues within 4Å: Chain H: S.17, D.40, D.126 Ligands: ADP.20, ALF.21 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:S.17, H2O.70, H2O.70, H2O.70

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: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

H
H

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Nitrogenase iron protein 1

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