› 5l06

Solution NMR

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position

Released:
DOI: 10.2210/pdb5l06/pdb
PDB entry 5l06 coloured by chain, ensemble of 9 models, front view.
PDB entry 5l06 coloured by chain, ensemble of 9 models, side view.
PDB entry 5l06 coloured by chain, ensemble of 9 models, top view.
Source organism: synthetic construct
Primary publication:
Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.
Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL
Nucleic Acids Res 46 10827-10839 (2018)
PMID: 30289469

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118972 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*CP*GP*(5CM)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 35%
Refinement method: simulated annealing
Expression system: Not provided

Quick links

Citations

6 review citations

The impact of epigenetic information on genome evolution.
Yi et al. (2021)
5 more

1 mention without citation

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.
Gruber et al. (2018)