SMTL ID : 6mp9.1

X-ray crystal structure of VioC bound to Fe(II), 2-oxo-5-guanidinopentanoic acid, and succinate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x JX7: 5-carbamimidamido-2-oxopentanoic acid(Non-covalent)

JX7.1: 17 residues within 4Å: Chain A: Q.116, L.135, V.136, S.137, L.144, G.145, W.146, H.147, E.149, D.201, S.203, D.247, D.249, F.250, R.313 Ligands: SIN.2, FE2.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.135, A:S.137, A:W.146, A:S.203, A:D.249, A:R.313 Water bridges: A:G.145, A:G.145, A:R.313, A:R.313 Salt bridges: A:D.247, A:D.249, A:R.313

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 13 residues within 4Å: Chain A: V.125, L.144, H.147, E.149, T.173, H.295, G.296, R.297, R.309, L.311, R.313 Ligands: JX7.1, FE2.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.297 Salt bridges: A:H.147, A:H.295, A:R.309, A:R.313

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

FE2.3: 5 residues within 4Å: Chain A: H.147, E.149, H.295 Ligands: JX7.1, SIN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.147, A:E.149, A:H.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dunham, N.P. et al., alpha-Amine Desaturation of d-Arginine by the Iron(II)- and 2-(Oxo)glutarate-Dependent l-Arginine 3-Hydroxylase, VioC. Biochemistry (2018)

Release Date

2018-11-21

Peptides

Alpha-ketoglutarate-dependent L-arginine hydroxylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent L-arginine hydroxylase