SMTL ID : 9c52.1

Cryo-EM structure of the Strand displacement Complex (I) of Yeast Mitochondrial DNA polymerase Gamma (MIP1) with downstream DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION

MG.1: 4 residues within 4Å: Chain A: D.666, V.667, D.865 Ligands: DTP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.666, A:V.667, A:D.865

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

DTP.2: 16 residues within 4Å: Chain A: D.666, V.667, D.668, S.669, E.670, E.671, K.700, R.718, K.722, Y.726, Y.730, D.865 Chain C: T.18, A.19 Ligands: MG.1, 2DT.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.726 Hydrogen bonds: A:D.666, A:S.669, A:E.670, A:E.670, A:E.670 Salt bridges: A:K.700, A:R.718, A:K.722, A:K.722, A:K.722 pi-Stacking: A:Y.726, A:Y.726

1 x 2DT: 3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE

2DT.3: 6 residues within 4Å: Chain A: R.629, H.864, K.921 Chain C: A.19 Chain D: G.23 Ligands: DTP.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.864 Hydrogen bonds: A:R.629, A:R.629 Salt bridges: A:K.921

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, A.R. et al., Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase. Nat Commun (2025)

Release Date

2025-03-19

Peptides

DNA polymerase gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase gamma

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