SMTL ID : 9emi.1

KOD-H4 DNA polymerase mutant in a ternary complex containing six HNA nucleotides and a non-hydrolyzable triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: Y.402, F.545, Y.583, Y.594, R.606 Chain B: A.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.606 Water bridges: A:Y.402 EDO.4: 5 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: G.8, C.9 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: E.500 Chain C: T.4, G.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.500

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.404, F.405, E.580 Ligands: XG4.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:F.405, A:E.580, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain A: D.542 Chain B: A.13 Ligands: XG4.3 No protein-ligand interaction detected (PLIP)

1 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.3: 18 residues within 4Å: Chain A: F.405, R.406, S.407, L.408, Y.409, P.410, R.460, K.487, N.491, G.495, T.541, D.542, E.580 Chain B: A.13 Chain C: C.3, T.4 Ligands: MG.2, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:S.407, A:Y.409, A:R.460, A:K.487, A:N.491, A:N.491 Water bridges: A:S.407 Salt bridges: A:R.460, A:K.464, A:K.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gutfreund, C. et al., Structural insights into a DNA polymerase reading the xeno nucleic acid HNA. Nucleic Acids Res. (2025)

Release Date

2024-11-13

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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