SMTL ID : 4b9m.1

Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dA DNA lesion -thymine basepair in the post- insertion site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.396, Y.397, D.573 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.396, A:Y.397, A:D.573

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

SO4.2: 3 residues within 4Å: Chain A: M.42, A.43, R.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.43 Salt bridges: A:R.86 SO4.3: 3 residues within 4Å: Chain A: H.425, R.445, K.449 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.425 Salt bridges: A:R.445, A:K.449 SO4.4: 6 residues within 4Å: Chain A: E.410, D.411, D.412, P.487, G.488, R.491 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.412, A:D.412, A:G.488 Water bridges: A:N.413 Salt bridges: A:R.491 SO4.5: 1 residues within 4Å: Chain A: R.522 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.522 SO4.6: 5 residues within 4Å: Chain A: Y.397, S.398, Q.399, D.608 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.399, A:Q.399, A:D.608 Water bridges: A:I.400 SO4.7: 5 residues within 4Å: Chain A: E.64, V.65, R.118, D.168, Y.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.168, A:R.178 Water bridges: A:K.193 Salt bridges: A:R.118, A:K.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gehrke, T.H. et al., Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-DNA Lesions. Nat.Chem.Biol. (2013)

Release Date

2013-04-17

Peptides

DNA POLYMERASE I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE I

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