SMTL ID : 7jkl.2 (1 other biounit)

Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (3'-end base of the primer strand is 2',3'-dideoxy-terminated).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.114, E.116, H.169 Ligands: CA.2, DTP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:D.114, A:E.116, H2O.1 CA.2: 6 residues within 4Å: Chain A: D.114, E.116, D.280 Chain C: G.13 Ligands: CA.1, DTP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.114, A:E.116, A:E.116, A:D.280

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

DTP.3: 19 residues within 4Å: Chain A: G.74, R.76, Y.100, D.114, E.116, S.160, S.167, H.169, V.283, R.288, N.289, F.290, R.291, K.297 Chain B: G.3, C.4 Chain C: G.13 Ligands: CA.1, CA.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.100, A:N.289 Hydrogen bonds: A:R.76, A:E.116, A:S.160, A:S.167, A:R.288, A:R.291 Water bridges: A:E.116, A:H.169 Salt bridges: A:H.169, A:R.291, A:R.291, A:K.297, A:K.297, A:K.297 pi-Cation interactions: A:R.76

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: E.101, L.158, H.169, I.171, F.290, R.291, L.292, Y.293, L.304, S.330, L.331, V.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.101, A:H.169, A:S.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Nat Commun (2021)

Release Date

2021-06-30

Peptides

DNA-directed primase/polymerase protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA-directed primase/polymerase protein

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