SMTL ID : 2ia6.1 (1 other biounit)

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: F.37, S.40, G.41, R.331 Ligands: PO4.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.41, A:R.331 PO4.2: 2 residues within 4Å: Chain A: R.331 Ligands: PO4.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.332 Salt bridges: A:R.331

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105 CA.4: 2 residues within 4Å: Chain A: A.181, I.186 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.181, A:I.186, H2O.1, H2O.6

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 14 residues within 4Å: Chain A: D.7, F.8, Y.10, F.11, T.45, Y.48, R.51, A.57, G.58, D.105, E.106, K.159 Chain B: A.13 Ligands: CA.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.10, A:F.11, A:D.105 Water bridges: A:D.7, A:D.9, A:Y.12, A:Y.12, A:K.152, A:K.152, A:D.156 Salt bridges: A:R.51, A:R.51, A:K.159, A:K.159

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain B: G.5, A.6 Chain C: C.14 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain B: G.3, G.4 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain B: G.4, G.5 Chain C: C.14, C.15 Ligands: EDO.6 No protein-ligand interaction detected (PLIP)

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

BAP.9: 4 residues within 4Å: Chain B: T.12, A.13 Chain C: G.5, A.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauer, J. et al., A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-09-11

Peptides

DNA polymerase IV: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase IV

Related Entries With Identical Sequence