SMTL ID : 8v7h.1

Human DNA polymerase eta-DNA-araC-ended primer ternary complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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: K.3, DTP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.116, A:E.119, A:E.119 Water bridges: A:R.64 Salt bridges: A:K.227

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: K.3, DTP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

1 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-CAR.1, CA.2, DTP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.118, A:E.119

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

DTP.4: 18 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, D.118, K.234 Chain B: T.4, G.5 Ligands: DA-DG-DC-DG-DT-DC-DA-CAR.1, CA.2, K.3 17 PLIP interactions: 17 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:R.64, A:R.64 Salt bridges: A:R.58, A:R.58, A:R.64, 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:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion. 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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