SMTL ID : 4b9s.1

Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion outside of the pre-insertion site.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 9 residues within 4Å: Chain A: E.68, Y.70, D.115, R.118, L.138, D.151, I.348, N.350, A.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.176, A:R.118, A:D.151, A:N.350, A:N.350, A:R.118, A:T.362 Salt bridges: A:K.174 Water bridges: A:Y.70, A:Q.351

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

SO4.2: 1 residues within 4Å: Chain A: R.420 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.427 Salt bridges: A:R.420 SO4.3: 4 residues within 4Å: Chain A: Y.397, S.398, Q.399 Ligands: MG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.399, A:Q.399 Water bridges: A:I.400, A:D.608 SO4.4: 3 residues within 4Å: Chain A: H.425, R.445, K.449 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.425 Salt bridges: A:R.445, A:K.449 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: 6 residues within 4Å: Chain A: E.64, V.65, V.66, R.118, D.168, Y.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.65 Water bridges: A:E.64, A:V.65 Salt bridges: A:R.118, A:K.193

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.396, Y.397, D.573 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.396, A:Y.397, A:D.573

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA POLYMERASE

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