SMTL ID : 4eyi.1

Human DNA polymerase iota incorporating dATP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x DG8- DG- DG- DG- DT- DC- DC- DT: DNA template(Non-covalent)

DG8-DG-DG-DG-DT-DC-DC-DT.1: 21 residues within 4Å: Chain A: L.99, R.103, S.276, P.299, Q.300, S.301, F.302, S.303, E.304, E.305, S.307, R.331, R.357 Ligands: DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DA-DG-DG-DA-DC-DC-DC.2, DTP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.307

1 x DA- DG- DG- DA- DC- DC- DC: DNA primer(Non-covalent)

DA-DG-DG-DA-DC-DC-DC.2: 26 residues within 4Å: Chain A: L.123, 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, Q.361 Ligands: DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DG8-DG-DG-DG-DT-DC-DC-DT.1, DTP.3, MG.4, MG.6 Protein-ligand interaction information (PLIP) not available

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

DTP.3: 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 Ligands: DG8-DG-DG-DG-DT-DC-DC-DT.1, DA-DG-DG-DA-DC-DC-DC.2, MG.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.39, A:T.65 Hydrogen bonds: A:C.37, A:F.38, A:Y.39, A:T.65, A:T.65, A:Y.68 Water bridges: A:E.127 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.34, D.126, E.127 Ligands: DA-DG-DG-DA-DC-DC-DC.2, DTP.3, MG.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.126, A:E.127 MG.5: 5 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: DTP.3, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 MG.6: 4 residues within 4Å: Chain A: K.237, I.239, I.242 Ligands: DA-DG-DG-DA-DC-DC-DC.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.237, A:I.242, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirouac, K.N. et al., Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase. Nucleic Acids Res. (2013)

Release Date

2013-01-09

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase iota

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