SMTL ID : 7olo.1

Dioxygenase AsqJ mutant (V72I) in complex with 2b and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.134, D.136, H.211 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.134, A:D.136, A:H.211 NI.7: 4 residues within 4Å: Chain B: H.134, D.136, H.211 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.134, B:D.136, B:H.211

2 x CO0: (3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione(Non-covalent)

CO0.2: 13 residues within 4Å: Chain A: N.70, I.72, L.73, L.79, M.118, M.122, Q.131, H.134, D.136, M.137, F.139 Ligands: GOL.5, GOL.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.72, A:L.73, A:L.79, A:F.139 Hydrogen bonds: A:N.70, A:M.137 Water bridges: A:R.138, A:F.139, A:S.140 pi-Stacking: A:H.134 CO0.8: 13 residues within 4Å: Chain B: N.70, I.72, L.73, L.79, M.118, M.122, Q.131, H.134, D.136, M.137, F.139 Ligands: GOL.11, GOL.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.72, B:L.73, B:L.79, B:F.139 Hydrogen bonds: B:N.70, B:M.137 Water bridges: B:R.138, B:F.139, B:S.140 pi-Stacking: B:H.134

2 x BR: BROMIDE ION(Non-covalent)

BR.3: 4 residues within 4Å: Chain A: T.172, G.213, R.223, L.225 Ligand excluded by PLIP BR.9: 4 residues within 4Å: Chain B: T.172, G.213, R.223, L.225 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: L.73, S.74, T.77, Q.131 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: L.73, S.74, T.77, Q.131 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: I.72, P.132, F.139 Chain B: R.271 Ligands: CO0.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.271, B:R.271 GOL.6: 7 residues within 4Å: Chain A: Q.131, H.134, D.136, N.157, H.211 Ligands: NI.1, CO0.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.131 GOL.11: 5 residues within 4Å: Chain A: R.271 Chain B: I.72, P.132, F.139 Ligands: CO0.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.271, A:R.271 GOL.12: 7 residues within 4Å: Chain B: Q.131, H.134, D.136, N.157, H.211 Ligands: NI.7, CO0.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Auman, D. et al., Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ. J.Am.Chem.Soc. (2022)

Release Date

2022-06-01

Peptides

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ

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