SMTL ID : 4b9l.1

Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 8 residues within 4Å: Chain A: E.68, Y.70, D.115, R.118, L.138, D.151, I.348, N.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.118, A:D.151, A:N.350, A:N.350, A:R.118 Water bridges: A:R.118, A:Q.351

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.396, Y.397, D.573 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.397, H2O.6

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

SO4.3: 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 SO4.4: 3 residues within 4Å: Chain A: H.425, R.445, K.449 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.399, A:H.425 Salt bridges: A:R.445, A:K.449 SO4.5: 3 residues within 4Å: Chain A: E.249, E.375, K.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.375 SO4.6: 1 residues within 4Å: Chain A: R.522 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.522

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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