SMTL ID : 8ppv.1

Intermediate conformer of Pyrococcus abyssi DNA polymerase D (PolD) bound to a primer/template substrate containing three consecutive mismatches

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.403, H.405, D.447, H.605 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.403, A:D.447, A:H.605 MG.2: 5 residues within 4Å: Chain A: D.447, N.493, H.540, H.603 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.447, A:H.603 MG.6: 3 residues within 4Å: Chain B: N.954, D.956, D.958 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.956, B:D.958, B:D.958

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.706, C.709, C.718, C.721 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.706, B:C.709, B:C.718, B:C.721 ZN.4: 4 residues within 4Å: Chain B: C.731, C.734, C.750, C.753 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.731, B:C.734, B:C.750, B:C.753 ZN.5: 4 residues within 4Å: Chain B: C.1123, C.1126, C.1139, C.1142 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1123, B:C.1139, B: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: A
DP2: B
DNA polymerase sliding clamp: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

DNA polymerase II small subunit

DP2

DNA polymerase sliding clamp

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