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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.7, F.8, D.105 Ligands: ATP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.7, A:F.8, A:D.105 CA.2: 5 residues within 4Å: Chain A: D.7, E.106, K.152 Chain B: A.13 Ligands: ATP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.7, A:E.106, H2O.6 CA.3: 2 residues within 4Å: Chain A: A.181, I.186 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.181, H2O.6, H2O.7, H2O.7, H2O.7

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

ATP.4: 17 residues within 4Å: Chain A: D.7, F.8, D.9, Y.10, F.11, Y.12, A.44, T.45, Y.48, R.51, A.57, D.105, K.159 Chain B: A.13 Chain C: T.4 Ligands: CA.1, CA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.12 Hydrogen bonds: A:Y.10, A:F.11, A:Y.12, A:T.45, A:Y.48, A:Y.48, A:Y.48 Salt bridges: A:R.51, A:R.51, A:K.159, A:K.159

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: P.184, G.185, Y.224 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain B: G.3, G.4 No protein-ligand interaction detected (PLIP) GOL.9: 4 residues within 4Å: Chain B: G.2, G.3 Chain C: C.16, C.17 No protein-ligand interaction detected (PLIP)

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

BAP.7: 5 residues within 4Å: Chain A: K.78, E.271, Y.274, K.275 Chain C: G.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.271, A:Y.274, A:Y.274, A:K.275 Hydrogen bonds: A:K.78, A:K.275 Water bridges: A:E.271 pi-Stacking: A:Y.274

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

EDO.8: 4 residues within 4Å: Chain B: A.7, G.8 Chain C: T.12, C.13 No protein-ligand interaction detected (PLIP)

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
B

DNA polymerase IV

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