› 1yzd

X-ray diffraction
2.35Å resolution

Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair

Released:
DOI: 10.2210/pdb1yzd/pdb
PDB entry 1yzd coloured by chain, front view.
PDB entry 1yzd coloured by chain, side view.
PDB entry 1yzd coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA.
Gherghe CM, Krahn JM, Weeks KM
J Am Chem Soc 127 13622-8 (2005)
PMID: 16190727

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-196277 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
RNA 5'-R(*GP*CP*AP*GP*AP*(A5M)P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3' Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 16 nucleotides
Theoretical weight: 5.1 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
1 modified residue:
Ligand A5M 3 x A5M

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3121
Unit cell:
a: 43Å b: 43Å c: 121Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.265 0.236 0.292
Expression system: Not provided

Quick links

Citations

1 review citation

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)
6 other articles

2 mentions without citation

Click modification of RNA at adenosine: structure and reactivity of 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenosine in RNA.
Phelps et al. (2014)
1 more