SMTL ID : 9eqf.1

Crystal structure of the L-arginine hydroxylase VioC MeHis316, bound to Fe(II), L-arginine, and succinate

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: 6 residues within 4Å: Chain A: H.204, E.206, H.352, R.370 Ligands: SIN.2, ARG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.204, A:E.206 FE2.6: 6 residues within 4Å: Chain B: H.204, E.206, H.352, R.370 Ligands: SIN.7, ARG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.204, B:E.206

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 15 residues within 4Å: Chain A: V.182, S.194, L.201, H.204, E.206, V.217, L.219, T.230, H.352, G.353, R.354, R.366, L.368, R.370 Ligands: FE2.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.230 Salt bridges: A:R.366, A:R.370 SIN.7: 15 residues within 4Å: Chain B: V.182, S.194, L.201, H.204, E.206, V.217, L.219, T.230, H.352, G.353, R.354, R.366, L.368, R.370 Ligands: FE2.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.230 Salt bridges: B:R.366, B:R.370

2 x ARG: ARGININE(Non-covalent)

ARG.3: 18 residues within 4Å: Chain A: Q.173, L.192, V.193, S.194, L.201, G.202, W.203, H.204, E.206, D.258, D.259, S.260, D.304, G.305, D.306, F.307, R.370 Ligands: FE2.1 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.201 Hydrogen bonds: A:Q.173, A:L.192, A:S.194, A:E.206, A:D.306 Water bridges: A:G.202, A:G.202, A:G.202, A:D.207, A:G.305, A:R.370, A:R.370, A:R.370, R.3 Salt bridges: A:D.304, A:D.306, A:R.370 ARG.8: 18 residues within 4Å: Chain B: Q.173, L.192, V.193, S.194, L.201, G.202, W.203, H.204, E.206, D.258, D.259, S.260, D.304, G.305, D.306, F.307, R.370 Ligands: FE2.6 18 PLIP interactions: 1 Ligand-Ligand interactions, 17 interactions with chain B Water bridges: R.8, B:G.202, B:G.202, B:G.202, B:D.207, B:G.305, B:R.370, B:R.370, B:R.370 Hydrophobic interactions: B:L.201 Hydrogen bonds: B:Q.173, B:L.192, B:S.194, B:E.206, B:D.306 Salt bridges: B:D.304, B:D.306, B:R.370

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

EDO.4: 2 residues within 4Å: Chain A: H.190, Q.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.199, A:Q.199 Water bridges: A:H.190 EDO.9: 2 residues within 4Å: Chain B: H.190, Q.199 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.199, B:Q.199 Water bridges: B:H.190

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: R.58, P.59, W.60, Y.333, E.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.58, A:E.334, A:E.334 Water bridges: A:R.58 PEG.10: 5 residues within 4Å: Chain B: R.58, P.59, W.60, Y.333, E.334 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.58, B:E.334, B:E.334 Water bridges: B:R.58, B:E.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hardy, F.J. et al., Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code. Acs Catalysis (2024)

Release Date

2024-07-31

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

Related Entries With Identical Sequence