SMTL ID : 8epz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 7 residues within 4Å: Chain A: C.57, C.125, D.126, H.197, C.198, A.204 Chain B: W.28 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.57, A:C.125, A:C.198 FES.6: 8 residues within 4Å: Chain A: W.28 Chain B: C.57, T.90, C.125, D.126, H.197, C.198, A.204 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.57, B:C.125, B:C.198

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: E.89, D.126, K.127, N.276, E.449 Ligands: CO2.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.89, A:E.89, A:D.126, A:E.449 MN.7: 6 residues within 4Å: Chain B: E.89, D.126, K.127, T.203, E.449 Ligands: CO2.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.89, B:E.89, B:D.126, B:E.449

3 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.3: 11 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: MN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.203, A:T.203, A:N.276, A:G.477, A:T.478 CO2.4: 4 residues within 4Å: Chain A: I.24, W.28, H.575 Chain B: S.476 No protein-ligand interaction detected (PLIP) CO2.8: 11 residues within 4Å: Chain B: E.89, D.126, K.127, G.202, T.203, A.204, N.276, E.449, S.476, G.477 Ligands: MN.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.203, B:T.203, B:A.204, B:N.276, B:G.477

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

BCT.5: 7 residues within 4Å: Chain A: W.168, E.449, S.476, T.478 Chain B: I.24, W.28, H.575 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.478, B:H.575

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

2023-02-22

Peptides

Dihydroxyacid dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroxyacid dehydratase

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