SMTL ID : 9emf.1

KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing one HNA nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.568, L.571, G.573 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.573, H2O.1, H2O.1 MG.2: 5 residues within 4Å: Chain A: Y.37, Y.39, K.73, E.111, Y.362 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.39, A:E.111 MG.3: 5 residues within 4Å: Chain A: E.111, Y.112, D.113, N.370, R.503 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.113 MG.4: 6 residues within 4Å: Chain A: S.419, D.421, G.447, F.448, I.449, P.450 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.421, A:D.421 MG.5: 4 residues within 4Å: Chain A: N.424, G.438, H.439, R.440 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.438, A:H.439

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: E.354, K.371, H.496, A.502, R.503 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.371, A:K.371, A:R.503

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: R.266, I.488 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.266 GOL.9: 5 residues within 4Å: Chain B: G.8, C.9 Chain C: G.7, G.8, C.9 No protein-ligand interaction detected (PLIP)

1 x 6BX: (2S)-2-hydroxy-3-(morpholin-4-yl)propane-1-sulfonic acid(Non-covalent)

6BX.8: 8 residues within 4Å: Chain A: Y.402, F.545, E.580, Y.583, Y.594, T.604, R.606 Chain B: A.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.580, A:Y.583

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gutfreund, C. et al., Crystallographic Insights into a Mutant Archaeal B-Family Polymerase processing HNA. To Be Published

Release Date

2025-09-24

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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