SMTL ID : 3oha.1

Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 19 residues within 4Å: Chain A: D.37, M.38, N.39, A.40, F.41, F.42, I.67, A.68, Y.71, R.74, R.80, D.162, K.286 Chain B: C.11 Chain C: T.1, G.2, G.3 Ligands: MG.5, MG.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.42 Hydrogen bonds: A:N.39, A:A.40, A:F.41, A:F.42, A:Y.71, A:R.80, A:R.80 Water bridges: A:D.37, A:R.74, A:R.74, A:R.74, A:K.286, A:K.286, A:K.286 Salt bridges: A:R.74, A:K.286 pi-Cation interactions: A:R.80

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: P.216, E.217, K.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.217, A:K.218 SO4.3: 3 residues within 4Å: Chain A: S.453, R.463 Chain B: C.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.453 Water bridges: A:S.451, A:S.451, A:S.451, A:T.509 Salt bridges: A:R.463 SO4.4: 3 residues within 4Å: Chain A: S.21, P.22, S.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:S.23

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.37, M.38, D.162 Ligands: DCP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.37, A:M.38, A:D.162 MG.6: 5 residues within 4Å: Chain A: D.37, D.162, E.163 Chain B: C.11 Ligands: DCP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.37, A:E.163, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silverstein, T.D. et al., Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta. Structure (2010)

Release Date

2010-12-22

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

Related Entries With Identical Sequence