Abortive ternary complex crystal structure of DNA polymerase beta with 8OG-dc base pair at the primer terminus and flipped out da

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

Ligands and binding sites

• SFV · [[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methylphosphonic acid · ligand · chains A, T, P
• MG · Magnesium ion · metal · 2 copies · chains A, P
• NA · Sodium ion · metal · 2 copies · chains A, P, D
• CL · Chloride ion · ion · 2 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 724 Ų buried · 16 hydrogen bonds · protein-nucleic
• A–P · 483 Ų buried · 10 hydrogen bonds · protein-nucleic
• T–P · 460 Ų buried · 42 hydrogen bonds · nucleic-nucleic
• A–D · 369 Ų buried · 7 hydrogen bonds · protein-nucleic
• T–D · 228 Ų buried · 23 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

• 6W2M · Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair… · the same entry in another collection · chain A against A, TM-score 1.00
• P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P06746
• Elsewhere: RCSB PDB 6W2M · PDBe 6W2M · UniProt P06746