SMTL ID : 6aln.1

VioC L-arginine hydroxylase bound to Fe(II), 3S-hydroxy-L-arginine, and 2OG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

AKG.1: 13 residues within 4Å: Chain A: V.182, L.201, H.204, E.206, L.219, T.230, H.352, R.354, R.366, L.368, R.370 Ligands: FE2.2, ZZU.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.201 Water bridges: A:R.354 Salt bridges: A:H.352, A:R.366, A:R.370 AKG.4: 13 residues within 4Å: Chain B: V.182, L.201, H.204, E.206, L.219, T.230, H.352, R.354, R.366, L.368, R.370 Ligands: FE2.5, ZZU.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.201 Water bridges: B:R.354 Salt bridges: B:H.352, B:R.366, B:R.370

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

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

2 x ZZU: (2S,3S)-3-HYDROXYARGININE(Non-covalent)

ZZU.3: 15 residues within 4Å: Chain A: Q.173, L.192, V.193, S.194, L.201, H.204, E.206, D.258, S.260, D.304, D.306, F.307, R.370 Ligands: AKG.1, FE2.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.173, A:Q.173, A:S.194, A:E.206, A:S.260, A:D.306, A:R.370, A:R.370 Water bridges: A:T.205, A:D.207 Salt bridges: A:D.258, A:D.304, A:R.370 pi-Cation interactions: A:H.204 ZZU.6: 15 residues within 4Å: Chain B: Q.173, L.192, V.193, S.194, L.201, H.204, E.206, D.258, S.260, D.304, D.306, F.307, R.370 Ligands: AKG.4, FE2.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.173, B:Q.173, B:S.194, B:E.206, B:S.260, B:D.306, B:D.306, B:R.370, B:R.370 Water bridges: B:T.205, B:D.207 Salt bridges: B:D.258, B:D.304, B:R.370 pi-Cation interactions: B:H.204

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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