DNA polymerase mu, 8-OXODGTP:AT product state ternary complex, 10 mm MG2+ (2160MIN)

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 15% strand (DSSP).

Ligands and binding sites

• NA · Sodium ion · metal · 2 copies · chains A, P
• MG · Magnesium ion · metal · chains A, P
• CL · Chloride ion · ion · chains A, D
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, P
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 1 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 670 Ų buried · 15 hydrogen bonds · protein-nucleic
• A–P · 570 Ų buried · 15 hydrogen bonds · protein-nucleic
• A–D · 384 Ų buried · 16 hydrogen bonds · protein-nucleic
• T–P · 250 Ų buried · 15 hydrogen bonds · nucleic-nucleic
• T–D · 196 Ų buried · 15 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent, 1 modified (additive adduct, nucleotide modification).

Compared structures

• 7KTN · DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10 mM Mg2+ (2160min) · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NP87 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9NP87) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9NP87
• Elsewhere: RCSB PDB 7KTN · PDBe 7KTN · UniProt Q9NP87