SMTL ID : 9en0.1

KOD-H4 DNA polymerase mutant in a unproductive binary complex with DNA:DNA containing six HNA nucleotides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: A.141, I.142, A.143, S.161, S.312 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.161, A:S.312 MG.2: 6 residues within 4Å: Chain A: G.211, D.212, N.213, F.214, F.216, A.217 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.211 MG.3: 5 residues within 4Å: Chain A: E.111, Y.112, D.113, N.370, R.503 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: Y.37, Y.39, E.111, R.119, Y.362 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.37, A:Y.39, A:E.111

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.17, D.235, S.237, K.240, K.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17, A:R.17, A:D.235, A:S.237, A:K.240 GOL.6: 5 residues within 4Å: Chain A: D.113, E.354, W.355, K.371, R.503 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.354, A:E.354, A:R.503 GOL.7: 6 residues within 4Å: Chain A: D.4, K.118, E.251, S.340, W.342, D.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.251, A:S.340, A:D.343 GOL.8: 2 residues within 4Å: Chain B: G.7, G.8 No protein-ligand interaction detected (PLIP)

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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