DNA polymerase mu, 8-OXORGTP:CT reaction state ternary complex, 50 mm MN2+ (960 min)

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).

Ligands and binding sites

• 8GM · [(2R,3S,4R,5R)-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A, T, P
• 8GT · 8-oxo-guanosine-5'-triphosphate · ligand · chains A, P
• PPV · Pyrophosphate · ligand · chains A
• MN · Manganese (II) ion · metal · 7 copies · chains A, T, D
• NA · Sodium ion · metal · chains A, P
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, P, T
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 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, 1 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–T · 691 Ų buried · 16 hydrogen bonds · protein-nucleic
• A–P · 373 Ų buried · 12 hydrogen bonds · protein-nucleic
• A–D · 354 Ų buried · 12 hydrogen bonds · protein-nucleic
• T–P · 208 Ų buried · 14 hydrogen bonds · nucleic-nucleic
• T–D · 197 Ų buried · 17 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

• 6VFB · DNA Polymerase Mu, 8-oxorGTP:Ct Reaction State Ternary Complex, 50 mM Mn2+ (960 min) · the same entry in another collection · chain T against T, 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 6VFB · PDBe 6VFB · UniProt Q9NP87