Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 12% 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
• NA · Sodium ion · metal · 2 copies · chains A, P, D
• MG · Magnesium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 549 Ų buried · 13 hydrogen bonds · protein-nucleic
• T–P · 473 Ų buried · 44 hydrogen bonds · nucleic-nucleic
• A–D · 390 Ų buried · 9 hydrogen bonds · protein-nucleic
• A–P · 341 Ų buried · 9 hydrogen bonds · protein-nucleic
• T–D · 232 Ų buried · 22 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

• 4YMN · Structure of human DNA polymerase beta complexed with N7BG in the template base paired… · 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 0.93

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 4YMN · PDBe 4YMN · UniProt P06746