› 2fij

X-ray diffraction
1.19Å resolution

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)

Released:
DOI: 10.2210/pdb2fij/pdb
PDB entry 2fij coloured by chain, front view.
PDB entry 2fij coloured by chain, side view.
PDB entry 2fij coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
Li F, Sarkhel S, Wilds CJ, Wawrzak Z, Prakash TP, Manoharan M, Egli M
Biochemistry 45 4141-52 (2006)
PMID: 16566588

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-115256 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand NCO 3 x NCO
2 modified residues:
Ligand A2M 2 x A2M
Ligand UAR 2 x UAR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 32.277Å b: 32.469Å c: 66.749Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.157 0.169
Expression system: Not provided

Quick links

Citations

5 review citations

The structural diversity of artificial genetic polymers.
Anosova et al. (2016)
4 more

2 mentions without citation

Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications.
Liczner et al. (2021)
1 more