› 1nzg

X-ray diffraction
1.6Å resolution

Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine

Released:
DOI: 10.2210/pdb1nzg/pdb
PDB entry 1nzg coloured by chain, front view.
PDB entry 1nzg coloured by chain, side view.
PDB entry 1nzg coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects.
Prhavc M, Prakash TP, Minasov G, Cook PD, Egli M, Manoharan M
Org Lett 5 2017-20 (2003)
PMID: 12790517

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-114289 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 10 nucleotides
Theoretical weight: 3.18 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 3ME 2 x 3ME

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 25.26Å b: 44.11Å c: 45.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.192 0.224
Expression system: Not provided

Quick links

Citations

6 review citations

Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
Egli et al. (2007)
5 more

1 mention without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)