SMTL ID : 8v7j.1

Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 20 mM Mg2+ for 600s

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DG-DT-DC-DA-CAR.1: 28 residues within 4Å: Chain A: S.116, 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, G.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: MG.3, DTP.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.116, A:E.119 Water bridges: A:E.119, A:E.119, A:K.227 Salt bridges: A:K.227

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: MG.3, DTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.3: 6 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-CAR.1, MG.2, DTP.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1, H2O.1

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

DTP.4: 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: T.4, G.5 Ligands: DA-DG-DC-DG-DT-DC-DA-CAR.1, MG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.18, A:C.19, A:F.20, A:F.21, A:Y.55 Water bridges: A:R.58, A:R.58, A:R.58, A:R.64, A:E.119, A:E.119, A:E.119, A:E.119 Salt bridges: A:R.58, A:R.58, A:R.64, A:K.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 20 mM Mg2+ for 600s. To Be Published

Release Date

2024-05-15

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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