Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP with manganese in the active site

Structure

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

Ligands and binding sites

• 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · chains A, T, P
• MN · Manganese (II) ion · metal · 2 copies · chains A, P
• NA · Sodium ion · metal · 2 copies · chains A, P, D

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 · 807 Ų buried · 14 hydrogen bonds · protein-nucleic
• T–P · 480 Ų buried · 44 hydrogen bonds · nucleic-nucleic
• A–P · 396 Ų buried · 12 hydrogen bonds · protein-nucleic
• A–D · 375 Ų buried · 8 hydrogen bonds · protein-nucleic
• T–D · 239 Ų buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

• 4YMO · Structure of human DNA polymerase beta complexed with N7BG in the template opposite to… · 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 4YMO · PDBe 4YMO · UniProt P06746