SMTL ID : 8s87.1

KOD-H4 DNA polymerase mutant - apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: R.17, D.235, S.237, K.253 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.235 MG.2: 6 residues within 4Å: Chain A: F.258, D.259, P.262, V.263, S.345, R.346 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.259, A:S.345 MG.3: 4 residues within 4Å: Chain A: A.141, I.142, D.215 Ligands: SO4.17 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.215, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.404, F.405, R.406, E.578, E.580 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.404, A:E.580 MG.11: 8 residues within 4Å: Chain A: G.211, D.212, N.213, F.214, D.215, F.216, A.217, V.250 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.211, H2O.3 MG.12: 4 residues within 4Å: Chain A: K.199, D.202, R.234, R.255 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.202 MG.14: 7 residues within 4Å: Chain A: I.122, I.337, G.338, Q.339, W.355, F.356, R.359 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.337, A:W.355 MG.15: 5 residues within 4Å: Chain A: I.618, E.621, T.622, R.625, V.646 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.622 MG.16: 4 residues within 4Å: Chain A: Q.332, R.335, L.336, R.482 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Q.332

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: Y.7, P.90, Q.91, P.115, F.116, A.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.91, A:F.116 SO4.6: 8 residues within 4Å: Chain A: N.568, A.569, L.571, P.572, G.573, A.574, L.575, E.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.575 SO4.10: 4 residues within 4Å: Chain A: Y.402, F.545, Y.583, Y.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.583, A:Y.583 SO4.13: 3 residues within 4Å: Chain A: R.188, K.192, I.228 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.188, A:K.192 SO4.17: 5 residues within 4Å: Chain A: Y.209, N.210, F.214, D.215 Ligands: MG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.210, A:D.215

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

NA.7: 2 residues within 4Å: Chain A: G.429, E.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.429 NA.9: 3 residues within 4Å: Chain A: G.125, R.359, E.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.359, A:E.363 Water bridges: A:G.125

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: D.4, T.5, D.6, A.117, K.118, E.251, K.253, S.340, W.342, D.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.5, A:K.118, A:D.343 Water bridges: A:T.5

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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