SMTL ID : 1xc9.1

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 11 residues within 4Å: Chain C: E.29, N.30, D.76, K.78, R.79, L.99, D.112, I.309, F.310, N.311, A.313 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.329, C:N.329, C:D.76, C:R.79, C:Q.312, C:A.313 Hydrogen bonds: C:K.78, C:D.112, C:F.310, C:N.311, C:A.313, C:E.29, C:R.79, C:E.324

1 x BAP: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE(Non-covalent)

BAP.2: 11 residues within 4Å: Chain A: C.10 Chain B: G.5, C.6, A.7 Chain C: R.319, E.362, V.417, Y.418, Q.501, H.533, D.534 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:E.362, C:V.417, C:Y.418 Water bridges: C:L.320, C:Q.328 pi-Cation interactions: C:R.319

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

SO4.3: 3 residues within 4Å: Chain C: H.386, R.406, K.410 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.406, C:K.410 SO4.4: 1 residues within 4Å: Chain C: R.523 3 PLIP interactions: 3 interactions with chain C Water bridges: C:R.523, C:R.523 Salt bridges: C:R.523 SO4.5: 4 residues within 4Å: Chain C: K.2, M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.4 Salt bridges: C:R.47 SO4.6: 2 residues within 4Å: Chain C: T.12, E.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.13

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain C: D.357, Y.358 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:Y.358, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsu, G.W. et al., Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication. J.Biol.Chem. (2005)

Release Date

2004-12-14

Peptides

DNA polymerase I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA polymerase I

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