SMTL ID : 4fs1.1

Base pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: D.34, L.35, D.126 Ligands: TTP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.34, C:L.35, C:D.126 MG.2: 5 residues within 4Å: Chain A: C.17 Chain C: K.237, I.239, P.240, I.242 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:K.237, C:I.239, C:I.242, H2O.1 MG.3: 7 residues within 4Å: Chain C: S.106, R.122, G.124, F.125, D.126, E.127, N.128 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:G.124, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain C: S.154, G.155, H.156, Q.218, T.219, V.220 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.218, C:Q.218

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

TTP.5: 17 residues within 4Å: Chain A: C.18 Chain B: X.4, G.5 Chain C: D.34, L.35, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, D.126, K.214 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:D.36, C:C.37, C:F.38, C:Y.39, C:T.65, C:Y.68, C:D.126 Water bridges: C:D.34, C:F.125, C:E.127 Salt bridges: C:R.71, C:R.71, C:K.77, C:K.77, C:K.77, C:K.214 pi-Stacking: C:Y.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, L. et al., Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases. J.Biol.Chem. (2012)

Release Date

2012-08-29

Peptides

DNA polymerase iota: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase iota

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