SMTL ID : 9nkc.1

Dpo4 DNA polymerase (Wild Type) in complex with DNA containing an 8oxoG template lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.1: 8 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, D.105 Ligands: CA.2, DTP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.7, A:D.7, A:F.8, A:D.105 CA.2: 6 residues within 4Å: Chain A: D.7, D.105, E.106 Chain B: A.14 Ligands: CA.1, DTP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.7, A:D.105, A:D.105, A:E.106 CA.3: 4 residues within 4Å: Chain A: K.152 Chain B: G.13, A.14 Ligands: DTP.4 No protein-ligand interaction detected (PLIP)

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.4: 21 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, A.57, G.58, D.105, K.159 Chain B: G.13, A.14 Chain C: T.4, C.5 Ligands: CA.1, CA.2, CA.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.10 Water bridges: A:D.9 Salt bridges: A:R.51, A:K.159, A:K.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Disha, S.S. et al., Residues in the little finger domain of the Y-family Dpo4 DNA polymerase communicate to restrict synthesis past 8-oxoguanine lesions. Nucleic Acids Res. (2025)

Release Date

2025-09-24

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

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