› 8gzk

X-ray diffraction
2.94Å resolution

Crystal structure of Cd2+-bound DNA aptamer T10A mutant

Released:
DOI: 10.2210/pdb8gzk/pdb
PDB entry 8gzk coloured by chain, front view.
PDB entry 8gzk coloured by chain, side view.
PDB entry 8gzk coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Crystal structures and identification of novel Cd2+-specific DNA aptamer.
Liu H, Gao Y, Mathivanan J, Armour-Garb Z, Shao Z, Zhang Y, Zhao X, Shao Q, Zhang W, Yang J, Cao C, Li H, Sheng J, Gan J
OpenAccess logo Nucleic Acids Res 51 4625-4636 (2023)
PMID: 37013991

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-222925 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
25-mer DNA Chains: A, B
Molecule details ›
Chains: A, B
Length: 25 nucleotides
Theoretical weight: 7.7 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CD 2 x CD
Ligand BA 5 x BA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 28.708Å b: 136.379Å c: 51.133Å
α: 90° β: 104.39° γ: 90°
R-values:
R R work R free
0.236 0.233 0.289
Expression system: Not provided

Quick links

Citations

1 citations in other articles

Generation of an accurate CCSD(T)/CBS data set and assessment of DFT methods for the binding strengths of group I metal-nucleic acid complexes.
Boychuk et al. (2023)

1 mention without citation

Crystal structures and identification of novel Cd2+-specific DNA aptamer.
Liu et al. (2023)