SMTL ID : 6db2.1

X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 12 residues within 4Å: Chain A: V.124, L.143, H.146, E.148, T.172, H.294, G.295, R.296, R.308, L.310, R.312 Ligands: VVO.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.296 Salt bridges: A:H.146, A:H.294, A:R.308, A:R.312

1 x HRG: L-HOMOARGININE(Non-covalent)

HRG.2: 15 residues within 4Å: Chain A: Q.115, L.134, V.135, S.136, L.143, G.144, H.146, E.148, D.200, S.202, D.246, D.248, F.249, R.312 Ligands: VVO.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.143 Hydrogen bonds: A:Q.115, A:L.134, A:S.136, A:W.145, A:E.148, A:S.202, A:D.248, A:R.312, A:R.312 Water bridges: A:Q.116, A:G.144, A:G.144 Salt bridges: A:D.246, A:D.248, A:R.312

1 x VVO: oxovanadium(2+)(Non-covalent)

VVO.3: 6 residues within 4Å: Chain A: H.146, E.148, H.294, R.312 Ligands: SIN.1, HRG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.148, A:R.312

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: T.80, P.81, Y.303, D.304, G.305, R.306, D.307 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.303, A:D.304, A:G.305, A:D.307 EDO.5: 3 residues within 4Å: Chain A: E.257, A.260, A.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.257, A:E.257 Water bridges: A:A.261 EDO.6: 4 residues within 4Å: Chain A: A.75, A.76, L.77, G.78 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunham, N.P. et al., Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance. J. Am. Chem. Soc. (2018)

Release Date

2018-05-16

Peptides

Alpha-ketoglutarate-dependent L-arginine hydroxylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent L-arginine hydroxylase

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