SMTL ID : 4ccl.1

X-Ray structure of E. coli ycfD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: H.125, D.127, H.187 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.125, A:D.127, A:H.187 MN.2: 2 residues within 4Å: Chain A: D.11, H.16 No protein-ligand interaction detected (PLIP) MN.8: 2 residues within 4Å: Chain B: H.56, D.58 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.58 MN.9: 2 residues within 4Å: Chain B: H.329, D.349 No protein-ligand interaction detected (PLIP)

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: L.82, M.112, S.114, V.122, R.140, W.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.114, A:S.114 Water bridges: A:V.122, A:V.122 Salt bridges: A:R.140 SO4.4: 6 residues within 4Å: Chain A: H.329, P.331, A.332, F.347, D.349, A.350 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.332, A:A.350 Salt bridges: A:H.329 SO4.5: 3 residues within 4Å: Chain A: R.15, H.16, V.22 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.15, A:H.16 SO4.6: 4 residues within 4Å: Chain A: R.101, S.338, N.339, I.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.340 Salt bridges: A:R.101 SO4.7: 3 residues within 4Å: Chain A: E.222, G.225 Chain B: R.208 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.208 SO4.10: 6 residues within 4Å: Chain B: L.82, M.112, S.114, R.140, W.142, N.197 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.114 Water bridges: B:S.114, B:V.122, B:R.140, B:R.140, B:R.140, B:S.199 Salt bridges: B:R.140 SO4.11: 3 residues within 4Å: Chain B: R.15, H.16, V.22 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.15, B:H.16 SO4.12: 2 residues within 4Å: Chain B: N.339, I.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.340, B:I.340 SO4.13: 4 residues within 4Å: Chain A: D.241 Chain B: R.313, G.315, R.330 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.241, B:G.315 Water bridges: A:H.238 Salt bridges: B:R.330

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

2014-04-30

Peptides

50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

50S RIBOSOMAL PROTEIN L16 ARGININE HYDROXYLASE