SMTL ID : 6fea.1

A. vinelandii vanadium nitrogenase, turnover state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-2-2-2-mer

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 B: F.59 Ligands: D6N.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.56, A:H.423 Hydrogen bonds: A:T.82, A:Q.176, A:K.361 Water bridges: A:K.83, A:K.83, A:G.405, A:G.405, A:R.407, A:R.407, A:R.407 Salt bridges: A:K.83, A:K.361, A:H.423, A:H.423 HCA.12: 9 residues within 4Å: Chain D: C.52, L.56, K.83, Q.176, K.361, P.406, H.423 Chain E: F.59 Ligands: D6N.11 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.56, D:H.423 Hydrogen bonds: D:Q.176, D:K.361 Water bridges: D:E.46, D:K.83, D:K.83, D:G.405, D:G.405, D:R.407, D:R.407, D:R.407, D:H.423 Salt bridges: D:K.83, D:K.361, D:H.423, D:H.423

2 x D6N: FeV(Non-covalent)

D6N.2: 16 residues within 4Å: Chain A: V.57, K.83, Q.176, H.180, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423 Ligands: HCA.1, CO3.3 1 PLIP interactions: 1 interactions with chain A, Metal complexes: A:C.257 D6N.11: 16 residues within 4Å: Chain D: V.57, K.83, Q.176, H.180, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423 Ligands: HCA.12, CO3.13 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: D6N.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.335, A:G.337, A:R.339 CO3.13: 6 residues within 4Å: Chain D: T.335, G.336, G.337, P.338, R.339 Ligands: D6N.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.336, D:G.337, D:G.337

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 5 residues within 4Å: Chain A: R.47, G.48, S.175, Q.176, F.362 No protein-ligand interaction detected (PLIP) H2S.14: 5 residues within 4Å: Chain D: R.47, G.48, S.175, Q.176, F.362 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 2 residues within 4Å: Chain A: H.448 Chain E: H.379 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:H.448, E:H.379, H2O.90, H2O.90 ZN.9: 2 residues within 4Å: Chain B: H.379 Chain D: H.448 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:H.448, B:H.379, H2O.23, H2O.68

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

CLF.6: 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 B: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.31, B:C.56, B:C.56, B:C.115, A:C.49, A:C.75, A:C.75, A:C.138 Salt bridges: A:D.78 CLF.15: 19 residues within 4Å: Chain D: 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 D, 4 interactions with chain E, Salt bridges: D:D.78 Metal complexes: D:C.49, D:C.75, D:C.75, D:C.138, E:C.31, E:C.56, E:C.56, E:C.115

4 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain B: E.70 Chain E: D.314 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: B:E.70, E:D.314, H2O.26, H2O.31, H2O.76, H2O.88 MG.8: 2 residues within 4Å: Chain B: D.314 Chain E: E.70 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:E.70, B:D.314, H2O.26, H2O.37, H2O.77, H2O.83 MG.10: 1 residues within 4Å: Chain C: E.14 No protein-ligand interaction detected (PLIP) MG.16: 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., A bound reaction intermediate sheds light on the mechanism of nitrogenase. Science (2018)

Release Date

2018-03-28

Peptides

Nitrogenase protein alpha chain: AD
Vanadium nitrogenase beta subunit, vnfK: BE
Vanadium nitrogenase, delta subunit, VnfG: 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

Vanadium nitrogenase beta subunit, vnfK

Vanadium nitrogenase, delta subunit, VnfG

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