SMTL ID : 6alm.1

VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.204, E.206, H.352 Ligands: AKG.2, ARG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.204, A:E.206, A:H.352 FE2.4: 5 residues within 4Å: Chain B: H.204, E.206, H.352 Ligands: AKG.5, ARG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.204, B:E.206, B:H.352

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: V.182, S.194, L.201, H.204, E.206, T.230, H.352, G.353, R.354, R.366, L.368, R.370 Ligands: FE2.1, ARG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.201 Hydrogen bonds: A:S.194 Water bridges: A:R.354 Salt bridges: A:R.366, A:R.370 AKG.5: 14 residues within 4Å: Chain B: V.182, S.194, L.201, H.204, E.206, T.230, H.352, G.353, R.354, R.366, L.368, R.370 Ligands: FE2.4, ARG.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.201 Hydrogen bonds: B:S.194 Water bridges: B:R.354 Salt bridges: B:R.366, B:R.370

2 x ARG: ARGININE(Non-covalent)

ARG.3: 15 residues within 4Å: Chain A: L.192, V.193, S.194, L.201, G.202, H.204, E.206, D.258, S.260, D.304, D.306, F.307, R.370 Ligands: FE2.1, AKG.2 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.201 Hydrogen bonds: A:L.192, A:S.194, A:S.260, A:D.306 Water bridges: A:Q.173, A:G.202, A:G.202, A:W.203, A:E.206, A:D.258, A:R.370, R.3 Salt bridges: A:D.304, A:D.306, A:R.370 ARG.6: 15 residues within 4Å: Chain B: L.192, V.193, S.194, L.201, G.202, H.204, E.206, D.258, S.260, D.304, D.306, F.307, R.370 Ligands: FE2.4, AKG.5 16 PLIP interactions: 15 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.201 Hydrogen bonds: B:L.192, B:S.194, B:S.260, B:D.306 Water bridges: B:Q.173, B:G.202, B:G.202, B:W.203, B:E.206, B:D.258, B:R.370, R.6 Salt bridges: B:D.304, B:D.306, B:R.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, A.J. et al., Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase. J. Am. Chem. Soc. (2017)

Release Date

2017-09-06

Peptides

Alpha-ketoglutarate-dependent L-arginine hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Alpha-ketoglutarate-dependent L-arginine hydroxylase

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