SMTL ID : 4liv.1

Structure of YcfD, a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and succinic acid.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 4 residues within 4Å: Chain A: H.159, D.161, H.221 Ligands: SIN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.159, A:D.161, A:H.221 CO.3: 4 residues within 4Å: Chain B: H.159, D.161, H.221 Ligands: SIN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.159, B:D.161, B:H.221

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 10 residues within 4Å: Chain A: M.146, S.148, V.156, H.159, D.161, R.174, W.176, H.221, N.231 Ligands: CO.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.156, A:W.176 Hydrogen bonds: A:S.148 Water bridges: A:R.174 Salt bridges: A:H.159, A:R.174, A:H.221 SIN.4: 10 residues within 4Å: Chain B: M.146, S.148, V.156, H.159, D.161, R.174, W.176, H.221, N.231 Ligands: CO.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.156, B:W.176 Hydrogen bonds: B:S.148 Water bridges: B:R.174 Salt bridges: B:H.159, B:R.174, B:H.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)

Release Date

2014-05-14

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

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