SMTL ID : 3g6y.1

Ternary complex of DNA Polymerase iota:DNA:dTTP with an abasic site at the templating position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DA- DG- DG- DA- DC- DC- DOC: Primer DNA strand(Non-covalent)

DA-DG-DG-DA-DC-DC-DOC.1: 24 residues within 4Å: Chain A: L.123, G.124, E.127, K.207, I.239, P.240, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360 Chain B: G.5, G.6, G.7, T.8, C.9, C.10, T.11 Ligands: TTP.2, MG.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.125 Salt bridges: A:K.207

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.2: 18 residues within 4Å: Chain A: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, K.214 Chain B: G.5 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.39 Hydrogen bonds: A:L.35, A:C.37, A:F.38, A:Y.39 Water bridges: A:Q.59, A:K.77, A:F.125, A:K.214 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: TTP.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 MG.4: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, TTP.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:D.34, A:E.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nair, D.T. et al., DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota. Structure (2009)

Release Date

2009-05-12

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase iota

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