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Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group P21/n

Analyse Racemic crystal structure of A-DNA duplex formed from d(CCCGGG) in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6GN3
Type
DNA
Length
36 nucleotides
Chains
6
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
2.8
Molecule
DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
Ligands
TMO, CO, CL

Structure

x-ray diffraction · resolution 2.8 · 1 distinct chain.

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, C, D, E, FDNA (5'-D(*CP*CP*CP*GP*GP*G)-3')dna6——

Ligands and binding sites

  • TMO · trimethylamine oxide · ligand · 4 copies · chains A, B, F
  • CO · Cobalt (II) ion · metal · 2 copies · chains B, D
  • CL · Chloride ion · ion · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

12 interfaces between chains.

  • E–F · 324 Ų buried · 43 hydrogen bonds · nucleic-nucleic
  • A–B · 323 Ų buried · 32 hydrogen bonds · nucleic-nucleic
  • C–D · 318 Ų buried · 33 hydrogen bonds · nucleic-nucleic
  • D–F · 163 Ų buried · 4 hydrogen bonds · nucleic-nucleic
  • B–D · 144 Ų buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

  • 6GN3 · Racemic crystal structure of a-DNA duplex formed from D(CCCGGG) in space group P21/N · the same entry in another collection · chain A against A, TM-score 1.00

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