SMTL ID : 8e8g.1

Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 180s

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- U- DG: DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*U)-D(P*G)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-U-DG.1: 39 residues within 4Å: Chain A: D.16, F.20, F.21, Q.41, I.51, A.52, R.64, S.116, I.117, D.118, E.119, K.227, I.258, 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: T.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: MN.2, MN.3, DGT.4, DPO.5, MN.6 Protein-ligand interaction information (PLIP) not available

3 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 7 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DA-DG-DC-DG-DT-DC-DA-U-DG.1, MN.3, DGT.4, DPO.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MN.3: 7 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-U-DG.1, DA-DG-DC-DG-DT-DC-DA-U-DG.1, MN.2, DGT.4 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 MN.6: 3 residues within 4Å: Ligands: DA-DG-DC-DG-DT-DC-DA-U-DG.1, DGT.4, DPO.5 No protein-ligand interaction detected (PLIP)

1 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.4: 23 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, Q.41, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: T.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-U-DG.1, DA-DG-DC-DG-DT-DC-DA-U-DG.1, MN.2, MN.3, DPO.5, MN.6 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.16, A:M.17, A:C.19, A:F.20, A:F.21, A:Q.41, A:Q.41, A:Y.55, A:R.64, A:R.64 Water bridges: A:R.58, A:R.58 Salt bridges: A:R.58, A:R.58, A:K.234

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.5: 14 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, A.52, Y.55, R.58, D.118, K.234 Ligands: DA-DG-DC-DG-DT-DC-DA-U-DG.1, MN.2, DGT.4, MN.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.18, A:C.19, A:F.20, A:Y.55 Water bridges: A:R.58, A:R.58 Salt bridges: A:R.58, A:R.58, A:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Primer terminal ribonucleotide alters the active site dynamics of DNA Polymerase eta and reduce DNA synthesis fidelity. J.Biol.Chem. (2023)

Release Date

2023-02-01

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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