SMTL ID : 8boq.1

A. vinelandii Fe-nitrogenase FeFe protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x S5Q: FeFe cofactor(Non-covalent)

S5Q.1: 15 residues within 4Å: Chain A: V.56, K.82, H.179, Y.210, C.256, S.259, P.334, G.335, G.336, S.337, K.338, F.361, H.422 Ligands: HCA.2, O.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:C.256, A:H.422, O.4, O.4 S5Q.8: 16 residues within 4Å: Chain D: V.56, K.82, Q.175, H.179, Y.210, C.256, S.259, P.334, G.335, G.336, S.337, K.338, F.361, H.422 Ligands: HCA.9, O.10 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:C.256, D:H.422, O.10, O.10

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

HCA.2: 9 residues within 4Å: Chain A: C.51, K.82, Q.175, K.360, G.404, K.405, H.422 Chain B: F.47 Ligands: S5Q.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.422 Hydrogen bonds: A:K.360, A:K.405 Water bridges: A:K.82, A:K.82, A:Q.175, A:Q.175, A:Q.175, A:R.406, A:R.406, A:N.420, A:N.420 Salt bridges: A:K.82, A:K.360, A:H.422, A:H.422 HCA.9: 10 residues within 4Å: Chain D: C.51, T.81, K.82, Q.175, K.360, G.404, K.405, H.422 Chain E: F.47 Ligands: S5Q.8 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:H.422 Hydrogen bonds: D:Q.175, D:K.360, D:K.405 Water bridges: D:H.55, D:T.81, D:K.82, D:K.82, D:R.406, D:R.406, D:N.420, D:N.420 Salt bridges: D:K.82, D:K.360, D:H.422, D:H.422

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

CLF.3: 17 residues within 4Å: Chain A: C.48, Y.50, P.71, G.73, C.74, D.77, C.137, G.169 Chain B: C.19, P.21, G.41, G.43, C.44, F.47, T.102, C.103, S.142 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.19, B:C.44, B:C.44, B:C.103, A:C.48, A:C.74, A:C.74, A:C.137 Salt bridges: A:D.77 CLF.12: 18 residues within 4Å: Chain D: C.48, Y.50, P.71, G.73, C.74, D.77, C.137, G.169 Chain E: C.19, P.21, G.41, Q.42, G.43, C.44, F.47, T.102, C.103, S.142 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain E, Salt bridges: D:D.77 Metal complexes: D:C.48, D:C.74, D:C.74, D:C.137, E:C.19, E:C.44, E:C.44, E:C.103

2 x O: OXYGEN ATOM(Non-covalent)

O.4: 4 residues within 4Å: Chain A: V.56, H.179, F.361 Ligands: S5Q.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.179 O.10: 5 residues within 4Å: Chain D: V.56, Q.175, H.179, F.361 Ligands: S5Q.8 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.175, D:H.179

2 x H2S: HYDROSULFURIC ACID(Covalent)(Non-covalent)

H2S.5: 5 residues within 4Å: Chain A: R.46, G.47, S.174, Q.175, F.361 No protein-ligand interaction detected (PLIP) H2S.11: 5 residues within 4Å: Chain D: R.46, G.47, S.174, Q.175, F.361 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: Y.56, E.58, D.208 Chain E: D.300 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: B:E.58, E:D.300, H2O.16, H2O.22, H2O.43, H2O.49 MG.7: 4 residues within 4Å: Chain B: D.300 Chain D: K.412 Chain E: Y.56, E.58 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: B:D.300, E:E.58, H2O.16, H2O.24, H2O.45, H2O.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trncik, C. et al., Iron-only Fe-nitrogenase underscores common catalytic principles in biological nitrogen fixation. Nat Catal (2023)

Release Date

2023-06-14

Peptides

Nitrogenase protein alpha chain: AD
Fe-only nitrogenase, beta subunit: BE
Nitrogenase iron-iron protein delta chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Nitrogenase protein alpha chain

Fe-only nitrogenase, beta subunit

Nitrogenase iron-iron protein delta chain