› 6d4l

Hybrid

Joint X-ray/neutron structure of DNA oligonucleotide d(GTGGCCAC)2 with 2'-SeCH3 modification on Cyt5

Released:
DOI: 10.2210/pdb6d4l/pdb
PDB entry 6d4l coloured by chain, front view.
PDB entry 6d4l coloured by chain, side view.
PDB entry 6d4l coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.
Vandavasi VG, Blakeley MP, Keen DA, Hu LR, Huang Z, Kovalevsky A
Structure 26 1645-1650.e3 (2018)
PMID: 30244969

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-119717 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
DNA (5'-D(*GP*TP*GP*GP*(CSL)P*CP*AP*C)-3') Chain: A
Molecule details ›
Chain: A
Length: 8 nucleotides
Theoretical weight: 2.52 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand DOD 29 x DOD
1 modified residue:
Ligand CSL 1 x CSL

Experiments and Validation Details

Experimental Method: X-ray diffraction, Neutron Diffraction
X-ray source: RIGAKU MICROMAX-007 HF, ILL BEAMLINE LADI III
Spacegroup: P43212
Unit cell:
a: 42.695Å b: 42.695Å c: 24.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.242 0.276
Expression system: Not provided

Quick links

Citations

2 citation in other articles

Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase.
Gerlits et al. (2019)
1 more

1 mention without citation

Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA.
Vandavasi et al. (2018)