SMTL ID : 7olm.1

Dioxygenase AsqJ mutant (V72I) in complex with 2b-O-O and Tris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.134, D.136, H.211 Ligands: VJQ.2, TRS.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.134, A:D.136, A:H.211 NI.6: 5 residues within 4Å: Chain B: H.134, D.136, H.211 Ligands: VJQ.7, TRS.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.134, B:D.136, B:H.211

2 x VJQ: 3-[(S)-dioxidanyl(phenyl)methyl]-4-methyl-2-oxidanyl-1H-1,4-benzodiazepin-5-one(Non-covalent)

VJQ.2: 15 residues within 4Å: Chain A: N.70, I.72, L.73, L.79, M.118, M.122, Q.131, P.132, H.134, D.136, M.137, F.139, T.227 Ligands: NI.1, TRS.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.72, A:L.79, A:Q.131, A:P.132, A:F.139, A:T.227 Hydrogen bonds: A:N.70, A:M.137 Water bridges: A:R.138, A:F.139, A:S.140 pi-Stacking: A:H.134 VJQ.7: 15 residues within 4Å: Chain B: N.70, I.72, L.73, L.79, M.118, M.122, Q.131, P.132, H.134, D.136, M.137, F.139, T.227 Ligands: NI.6, TRS.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.72, B:L.79, B:Q.131, B:P.132, B:F.139, B:T.227 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 TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 11 residues within 4Å: Chain A: M.122, Q.131, H.134, D.136, N.157, L.159, T.172, H.211 Ligands: NI.1, VJQ.2, BR.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.131, A:Q.131, A:N.157 TRS.8: 11 residues within 4Å: Chain B: M.122, Q.131, H.134, D.136, N.157, L.159, T.172, H.211 Ligands: NI.6, VJQ.7, BR.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.131, B:Q.131, B:N.157

2 x BR: BROMIDE ION(Non-covalent)

BR.4: 5 residues within 4Å: Chain A: T.172, G.213, R.223, L.225 Ligands: TRS.3 Ligand excluded by PLIP BR.9: 5 residues within 4Å: Chain B: T.172, G.213, R.223, L.225 Ligands: TRS.8 Ligand excluded by PLIP

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

CL.5: 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

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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