› 4gs2

X-ray diffraction
1.9Å resolution

DNA Holliday junction stabilized by iodine halogen bond. I1J construct in related reference.

Released:
DOI: 10.2210/pdb4gs2/pdb
PDB entry 4gs2 coloured by chain, front view.
PDB entry 4gs2 coloured by chain, side view.
PDB entry 4gs2 coloured by chain, top view.
Source organisms:
Primary publication:
Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.
Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS
Biochemistry 52 4891-903 (2013)
PMID: 23789744

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117558 (preferred)
Entry contents:
2 distinct DNA molecules
Macromolecules (2 distinct):
DNA (5'-D(*CP*CP*GP*GP*TP*AP*(5IU)P*CP*GP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 10 nucleotides
Theoretical weight: 3.17 KDa
Source organism: Unidentified
Expression system: Not provided
DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.03 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5IU 1 x 5IU

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 65.739Å b: 25.187Å c: 37.171Å
α: 90° β: 110.88° γ: 90°
R-values:
R R work R free
0.235 0.235 0.261
Expression system: Not provided

Quick links

Citations

6 review citations

The Halogen Bond.
Cavallo et al. (2016)
5 more

1 mention without citation

Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences.
Oliva et al. (2017)