SMTL ID : 8ppu.1

Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: T.21 Chain C: D.447, N.493, H.540, H.603 Ligands: MG.2 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.447, C:H.540 MG.2: 6 residues within 4Å: Chain A: T.21 Chain C: D.403, H.405, D.447, H.605 Ligands: MG.1 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.403, C:H.405, C:D.447 MG.6: 3 residues within 4Å: Chain G: N.954, D.956, D.958 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.956, G:D.958

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain G: C.706, C.709, C.718, C.721 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.706, G:C.709, G:C.718, G:C.721 ZN.4: 5 residues within 4Å: Chain G: C.731, R.733, C.734, C.750, C.753 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.731, G:C.734, G:C.753 ZN.5: 4 residues within 4Å: Chain G: C.1123, C.1126, C.1139, C.1142 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.1123, G:C.1126, G:C.1139, G:C.1142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betancurt-Anzola, L. et al., Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun (2023)

Release Date

2023-12-20

Peptides

DNA polymerase II small subunit: C
DNA polymerase sliding clamp: DEF
DP2: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
C

E
D

F
E

G
B

DNA polymerase II small subunit

DNA polymerase sliding clamp

DP2

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