Crystal structure of klentaq mutant M747K in a closed ternary complex with a O6-MEG:BENZITP base pair

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).

Ligands and binding sites

• NZI · [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate · ligand · chains A, B, C
• MN · Manganese (II) ion · metal · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• ACT · Acetate ion · additive · 3 copies · chains A, C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1428 Ų buried · 22 hydrogen bonds · protein-nucleic
• A–B · 837 Ų buried · 28 hydrogen bonds · protein-nucleic
• B–C · 601 Ų buried · 57 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

• 5OXJ · Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
• P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P19821
• Elsewhere: RCSB PDB 5OXJ · PDBe 5OXJ · UniProt P19821