SMTL ID : 8ujt.1

Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite urea lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.1: 26 residues within 4Å: Chain A: S.116, D.118, E.119, K.227, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.380, L.384, R.385, R.386, C.387 Chain B: A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DZ4.2, MG.4 Protein-ligand interaction information (PLIP) not available

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.2: 19 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: X.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.16, A:C.19, A:F.20, A:F.21, A:Y.55, A:Y.55, A:R.58, A:R.64, A:D.118 Water bridges: A:R.58, A:R.58, A:S.116 Salt bridges: A:R.58, A:K.234

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: DZ4.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.4: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, DZ4.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tomar, R. et al., Replication Bypass of the N -(2-Deoxy-d-erythro-pentofuranosyl)-urea DNA Lesion by Human DNA Polymerase eta. Biochemistry (2024)

Release Date

2024-03-20

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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