SMTL ID : 8ej0.1

Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

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

FES.1: 9 residues within 4Å: Chain A: C.57, E.89, C.125, D.126, H.197, C.198, A.204 Chain B: W.28 Ligands: BCT.4 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.57, A:C.125, A:C.198 FES.5: 10 residues within 4Å: Chain A: W.28 Chain B: C.57, E.89, T.90, C.125, D.126, H.197, C.198, A.204 Ligands: BCT.7 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.57, B:C.125, B:C.198 FES.8: 9 residues within 4Å: Chain C: C.57, E.89, T.90, C.125, D.126, H.197, C.198, A.204 Chain D: W.28 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.57, C:C.125, C:D.126, C:C.198 FES.13: 10 residues within 4Å: Chain C: W.28 Chain D: C.57, E.89, T.90, C.125, D.126, H.197, C.198, A.204 Ligands: CO2.15 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.57, D:C.125, D:C.198

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: E.89, D.126, K.127, T.203, E.449 Ligands: BCT.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.89, A:D.126, A:E.449 MG.6: 7 residues within 4Å: Chain B: E.89, D.126, K.127, T.203, N.276, E.449 Ligands: BCT.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.89, B:E.449 MG.9: 6 residues within 4Å: Chain C: E.89, D.126, K.127, T.203, E.449 Ligands: BCT.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.89, C:D.126, C:E.449 MG.14: 6 residues within 4Å: Chain D: E.89, D.126, K.127, T.203, E.449 Ligands: CO2.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.89, D:E.89, D:D.126, D:E.449

6 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 8 residues within 4Å: Chain A: T.90, G.164, W.168, E.449, S.476 Chain B: W.28, H.575 Ligands: BCT.4 No protein-ligand interaction detected (PLIP) BCT.4: 13 residues within 4Å: Chain A: E.89, D.126, K.127, G.202, T.203, N.276, E.449, S.476, G.477, T.478 Ligands: FES.1, MG.2, BCT.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.89, A:E.449 BCT.7: 12 residues within 4Å: Chain B: E.89, D.126, K.127, G.202, T.203, N.276, E.449, S.476, G.477, T.478 Ligands: FES.5, MG.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.203, B:T.203, B:E.449, B:G.477, B:T.478 Water bridges: B:A.204 BCT.10: 3 residues within 4Å: Chain B: R.230, W.360 Chain C: K.155 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.155, C:R.157 BCT.11: 11 residues within 4Å: Chain C: E.89, D.126, K.127, G.202, T.203, N.276, E.449, S.476, G.477, T.478 Ligands: MG.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.203, C:T.203, C:E.449, C:G.477, C:T.478 BCT.12: 3 residues within 4Å: Chain C: P.94, M.538 Chain D: R.112 No protein-ligand interaction detected (PLIP)

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.15: 11 residues within 4Å: Chain D: E.89, D.126, K.127, G.202, T.203, E.449, S.476, G.477, T.478 Ligands: FES.13, MG.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.203, D:T.203, D:N.276, D:G.477, D:T.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bayaraa, T. et al., Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg. To Be Published

Release Date

2023-08-30

Peptides

Dihydroxyacid dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Dihydroxyacid dehydratase

Related Entries With Identical Sequence