SMTL ID : 4nub.1

Crystal structure of Escherichia coli ribosomal oxygenase YcfD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 3 residues within 4Å: Chain A: H.125, D.127, H.187 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.125, A:D.127, A:H.187, H2O.1, H2O.1 FE.3: 3 residues within 4Å: Chain B: H.125, D.127, H.187 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.125, B:D.127, B:H.187, H2O.3, H2O.3

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: E.301, E.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.301 GOL.4: 2 residues within 4Å: Chain B: E.301, E.372 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Staalduinen, L.M. et al., Structure and Functional Analysis of YcfD, a Novel 2-Oxoglutarate/Fe(2+)-Dependent Oxygenase Involved in Translational Regulation in Escherichia coli. J.Mol.Biol. (2014)

Release Date

2014-02-26

Peptides

50S ribosomal protein L16 arginine hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

50S ribosomal protein L16 arginine hydroxylase