SMTL ID : 9dqu.1

Product complex of DNA polymerase iota with Pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.1: 13 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, T.65, Y.68, R.71, K.77, D.126, K.214 Chain B: T.19 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:C.37, A:F.38, A:T.65, A:Y.68 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.214 POP.5: 13 residues within 4Å: Chain C: D.34, L.35, D.36, C.37, F.38, T.65, Y.68, R.71, K.77, D.126, K.214 Chain D: T.19 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:C.37, C:F.38, C:T.65, C:Y.68 Salt bridges: C:R.71, C:R.71, C:K.77, C:K.77, C:K.214

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Chain B: C.18, T.19 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:D.126, A:D.126, A:E.127, H2O.3 MG.3: 7 residues within 4Å: Chain A: D.34, L.35, D.126, K.214 Chain B: T.19 Ligands: POP.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 MG.4: 7 residues within 4Å: Chain A: K.237, I.239, P.240, G.241, I.242, G.243 Chain B: C.17 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.237, A:I.239, A:I.242, H2O.1, H2O.4 MG.6: 6 residues within 4Å: Chain C: D.34, D.126, E.127 Chain D: C.18, T.19 Ligands: MG.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.34, C:D.126, C:D.126, C:E.127, H2O.8 MG.7: 7 residues within 4Å: Chain C: D.34, L.35, D.126, K.214 Chain D: T.19 Ligands: POP.5, MG.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.34, C:L.35, C:D.126 MG.8: 7 residues within 4Å: Chain C: K.237, I.239, P.240, G.241, I.242, G.243 Chain D: C.17 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:K.237, C:I.239, C:I.242, H2O.5, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frevert, Z. et al., Visualizing DNA polymerase iota catalyze Hoogsteen-directed DNA synthesis. Nat Commun (2025)

Release Date

2025-07-09

Peptides

DNA polymerase iota: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

DNA polymerase iota

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