Structure of PDB 2ibk Chain A Binding Site BS02

Receptor Information

>2ibk Chain A (length=341) Species: 273057 (Saccharolobus solfataricus P2)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

Ligand information

>2ibk Chain E (length=17)

tcatgaatccttccccc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ibk A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): F37 G41 A42 G58 M76 K78 E79 G218 A220 K221 R242 K243 S244 G246 R247 I248 K275 L293 R331 R332 R336
• Binding residue (residue number reindexed from 1): F37 G41 A42 G58 M76 K78 E79 G218 A220 K221 R242 K243 S244 G246 R247 I248 K275 L293 R331 R332 R336

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0042276 error-prone translesion synthesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2ibk, PDBe:2ibk, PDBj:2ibk
• PDBsum: 2ibk
• PubMed: 17848527
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)