SMTL ID : 5n6y.1

Azotobacter vinelandii vanadium nitrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-oligomer

Ligands

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

HCA.1: 9 residues within 4Å: Chain A: C.52, L.56, K.83, Q.176, K.361, P.406, H.423 Chain E: F.59 Ligands: 8P8.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.56, A:H.423 Hydrogen bonds: A:Q.176 Water bridges: A:K.83, A:K.83, A:K.361, A:G.405, A:G.405, A:R.407, A:R.407 Salt bridges: A:K.83, A:K.361, A:K.361, A:H.423, A:H.423 HCA.9: 9 residues within 4Å: Chain B: F.59 Chain D: C.52, L.56, K.83, Q.176, K.361, P.406, H.423 Ligands: 8P8.10 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.56, D:H.423 Hydrogen bonds: D:Q.176 Water bridges: D:E.46, D:K.83, D:K.83, D:K.361, D:G.405, D:G.405, D:R.407, D:R.407 Salt bridges: D:K.83, D:K.361, D:K.361, D:H.423, D:H.423

2 x 8P8: C Fe7 S8 V(Non-covalent)

8P8.2: 14 residues within 4Å: Chain A: V.57, K.83, H.180, F.211, I.213, C.257, S.260, G.336, P.338, R.339, F.362, H.423 Ligands: HCA.1, CO3.3 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.257 8P8.10: 13 residues within 4Å: Chain D: V.57, K.83, H.180, F.211, C.257, S.260, G.336, P.338, R.339, F.362, H.423 Ligands: HCA.9, CO3.11 1 PLIP interactions: 1 interactions with chain D, Metal complexes: D:C.257

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 6 residues within 4Å: Chain A: T.335, G.336, G.337, P.338, R.339 Ligands: 8P8.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.335, A:G.336, A:R.339 CO3.11: 6 residues within 4Å: Chain D: T.335, G.336, G.337, P.338, R.339 Ligands: 8P8.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.336, D:G.337, D:R.339

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

CLF.4: 19 residues within 4Å: Chain A: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170 Chain E: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain E, Salt bridges: A:D.78 Metal complexes: A:C.49, A:C.75, A:C.75, A:C.138, E:C.31, E:C.56, E:C.56, E:C.115 CLF.5: 19 residues within 4Å: Chain B: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153 Chain D: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain D, Metal complexes: B:C.31, B:C.56, B:C.56, B:C.115, D:C.49, D:C.75, D:C.75, D:C.138 Salt bridges: D:D.78

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: D.314 Chain E: E.70 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: B:D.314, E:E.70, H2O.21, H2O.32, H2O.66, H2O.70 MG.7: 2 residues within 4Å: Chain B: E.70 Chain E: D.314 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:D.314, B:E.70, H2O.21, H2O.25, H2O.65, H2O.74 MG.8: 1 residues within 4Å: Chain C: E.14 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain F: E.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sippel, D. et al., The structure of vanadium nitrogenase reveals an unusual bridging ligand. Nat. Chem. Biol. (2017)

Release Date

2017-07-26

Peptides

Nitrogenase vanadium-iron protein alpha chain: AD
Nitrogenase vanadium-iron protein beta chain: BE
Nitrogenase vanadium-iron protein delta chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
E

E
B

C
C

F
F

Nitrogenase vanadium-iron protein alpha chain

Nitrogenase vanadium-iron protein beta chain

Nitrogenase vanadium-iron protein delta chain

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