SMTL ID : 9cu0.1

Azotobacter vinelandii 1:1:1 MoFeP:FeP:FeSII-Complex (C1 symmetry)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-1-mer

Ligands

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

HCA.1: 8 residues within 4Å: Chain A: G.95, R.96, Q.191, G.424, I.425, H.442 Chain B: R.105 Ligands: ICS.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.191, A:I.425 Salt bridges: A:K.426, A:H.442 HCA.6: 9 residues within 4Å: Chain C: G.95, R.96, Q.191, G.424, I.425, K.426, E.440, H.442 Ligands: ICS.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.191, C:I.425, C:H.442 Salt bridges: C:H.442

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

ICS.2: 13 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, C.275, S.278, I.355, G.356, G.357, R.359, F.381, H.442 Ligands: HCA.1 3 PLIP interactions: 3 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275, A:G.357 ICS.7: 13 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, C.275, S.278, I.355, G.356, G.357, R.359, F.381, H.442 Ligands: HCA.6 3 PLIP interactions: 3 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275, C:G.357

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 8 PLIP interactions: 4 interactions with chain B, 4 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 CLF.8: 15 residues within 4Å: Chain C: C.62, P.85, G.87, C.88, Y.91, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, C.153, S.188 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D, Salt bridges: C:E.153 Metal complexes: C:C.62, C:C.154, D:C.70, D:C.95, D:C.153, D:S.188

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, 3 interactions with chain B Metal complexes: D:R.108, D:E.109, B:D.353, B:D.353, B:D.357 FE.5: 6 residues within 4Å: Chain A: F.429, K.433 Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:R.108, B:E.109, B:E.109, D:D.353, D:D.357

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

ADP.9: 17 residues within 4Å: Chain E: G.12, G.13, I.14, G.15, K.16, S.17, T.18, T.19, D.40, V.212, P.213, R.214, D.215, V.218, Q.237, Y.241 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.13, E:G.15, E:K.16, E:S.17, E:S.17, E:T.18, E:T.18, E:D.215, E:Q.237, E:Y.241, E:Y.241 Salt bridges: E:K.16, E:K.42, E:K.42 ADP.12: 18 residues within 4Å: Chain E: M.157 Chain F: 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 Ligands: MG.13 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.13, F:I.14, F:G.15, F:S.17, F:T.18, F:T.18, F:N.186, F:P.213, F:D.215, F:E.222 Salt bridges: F:K.16

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 4 residues within 4Å: Chain E: S.17, D.40, K.42 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.13: 3 residues within 4Å: Chain F: S.17, D.40 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17

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

SF4.11: 12 residues within 4Å: Chain E: C.98, A.99, C.133, G.134, F.136 Chain F: G.97, C.98, A.99, C.133, G.134, F.136 Chain G: A.122 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

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.14: 9 residues within 4Å: Chain G: E.41, C.42, G.45, N.46, C.47, G.48, C.50, L.100, C.102 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.42, G:C.47, G:C.50, G:C.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narehood, S.M. et al., Structural basis for the conformational protection of nitrogenase from O 2 . Nature (2025)

Release Date

2025-01-15

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
Nitrogenase iron protein 1: EF
Protein FeSII: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Nitrogenase iron protein 1

Protein FeSII

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