SMTL ID : 7jk1.2 (1 other biounit)

Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 20 residues within 4Å: Chain A: G.74, R.76, Y.100, D.114, E.116, S.160, K.165, S.167, H.169, D.280, V.283, R.288, N.289, F.290, R.291, K.297 Chain B: G.12 Chain C: G.3, C.4 Ligands: CA.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.100 Hydrogen bonds: A:S.160, A:S.160, A:S.167, A:R.288, A:R.291 Salt bridges: A:K.165, A:K.165, A:K.165, A:H.169, A:R.291, A:R.291, A:K.297, A:K.297, A:K.297

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.114, E.116, K.165 Ligands: DCP.1 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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 13 residues within 4Å: Chain A: E.101, L.158, H.169, I.171, F.290, R.291, L.292, Y.293, L.304, F.327, S.330, L.331, V.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.169, A:R.291, A:Y.293, A:S.330, 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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