SMTL ID : 8v7b.1

Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex at pH7.0 (K+ MES) with 1 Ca2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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: 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: G.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: HF4.5, K.7 Protein-ligand interaction information (PLIP) not available

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.250 Water bridges: A:E.280, A:T.282, A:T.282 GOL.3: 3 residues within 4Å: Chain A: E.97, A.98, E.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.101 Water bridges: A:E.97, A:A.98, A:E.101 GOL.4: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP)

1 x HF4: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

HF4.5: 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: G.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.6, K.7 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:C.19, A:F.20, A:F.21, A:Y.55, A:Y.55, A:R.64 Water bridges: A:R.58, A:R.58, A:R.58, A:R.58, A:R.64, 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 pi-Cation interactions: A:R.64

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: HF4.5, K.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.16, A:D.16, A:M.17, A:D.118

1 x K: POTASSIUM ION(Non-covalent)

K.7: 6 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, HF4.5, CA.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:D.118, A:E.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Human DNA polymerase eta-DNA-dT primer araCTP insertion ternary complex 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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