SMTL ID : 9dr7.1

Product complex of DNA polymerase iota with 2 monophosphates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: L.35, D.36, C.37, Y.68, R.71, K.77, K.214 Chain B: T.19 Ligands: MG.2, PO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.37, A:Y.68 Salt bridges: A:R.71, A:K.77, A:K.214 PO4.5: 9 residues within 4Å: Chain A: C.37, F.38, T.65, R.71, K.77, D.126 Chain B: T.19 Ligands: PO4.1, MG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.38, A:T.65 Salt bridges: A:R.71, A:K.77 PO4.6: 10 residues within 4Å: Chain C: L.35, D.36, C.37, Y.68, R.71, K.77, K.214 Chain D: T.19 Ligands: MG.7, PO4.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:C.37, C:Y.68 Salt bridges: C:R.71, C:K.77, C:K.214 PO4.10: 9 residues within 4Å: Chain C: C.37, F.38, T.65, R.71, K.77, D.126 Chain D: T.19 Ligands: PO4.6, MG.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.38, C:T.65 Salt bridges: C:R.71, C:K.77

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.34, L.35, D.126 Chain B: T.19 Ligands: PO4.1, MG.3, PO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 MG.3: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Chain B: C.18, T.19 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.34, A:D.34, A:D.126, A:E.127 MG.4: 7 residues within 4Å: Chain A: K.237, E.238, I.239, P.240, G.241, I.242 Chain B: C.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:K.237, A:I.239, A:I.242 MG.7: 7 residues within 4Å: Chain C: D.34, L.35, D.126 Chain D: T.19 Ligands: PO4.6, MG.8, PO4.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.34, C:L.35, C:D.126 MG.8: 6 residues within 4Å: Chain C: D.34, D.126, E.127 Chain D: C.18, T.19 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.34, C:D.34, C:D.126, C:E.127 MG.9: 7 residues within 4Å: Chain C: K.237, E.238, I.239, P.240, G.241, I.242 Chain D: C.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:K.237, C:I.239, C:I.242

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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