SMTL ID : 8s84.1

KOD-H4 DNA polymerase mutant in a ternary complex with DNA/DNA and non-hydrolyzable triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.460, K.487 Ligands: XG4.4 No protein-ligand interaction detected (PLIP) MG.2: 5 residues within 4Å: Chain A: D.404, F.405, D.542 Ligands: MG.3, XG4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542 MG.3: 6 residues within 4Å: Chain A: Y.402, D.404, D.542 Chain B: A.13 Ligands: MG.2, XG4.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.1 MG.5: 4 residues within 4Å: Chain A: D.4, E.251, S.340, D.343 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.4, A:D.343 MG.6: 5 residues within 4Å: Chain A: E.111, A.368, P.369, N.370, R.503 No protein-ligand interaction detected (PLIP)

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

XG4.4: 20 residues within 4Å: Chain A: D.404, F.405, S.407, L.408, Y.409, P.410, R.460, K.487, N.491, Y.494, G.495, D.542, E.578, E.580 Chain B: A.13 Chain C: C.3, T.4 Ligands: MG.1, MG.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:L.408, A:Y.409, A:R.460, A:K.487, A:K.487, A:K.487, A:N.491, A:N.491, A:G.495, A:E.578, A:E.580 Salt bridges: A:K.487

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 3 residues within 4Å: Chain A: E.500 Chain C: T.4, G.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.500

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.8: 5 residues within 4Å: Chain A: Y.402, Y.583, Y.594, T.604, R.606 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.583, A:Y.583 pi-Stacking: A:Y.402, A:F.545

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain B: C.6, G.7, G.8 Chain C: G.8, C.9 No protein-ligand interaction detected (PLIP) GOL.10: 3 residues within 4Å: Chain C: T.12, G.13, G.14 No protein-ligand interaction detected (PLIP)

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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