Structure of PDB 2rdj Chain B Binding Site BS01

Receptor Information

>2rdj Chain B (length=341) Species: 273057 (Saccharolobus solfataricus P2)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

Ligand information

>2rdj Chain E (length=14)

gggacccttcgaat

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2rdj Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): F11 Y12 A44 T45 A57 D105 E106 K152 P184 G185 G187 I189 T190 V296 S297 R298
• Binding residue (residue number reindexed from 1): F11 Y12 A44 T45 A57 D105 E106 K152 P184 G185 G187 I189 T190 V296 S297 R298

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:2rdj, PDBe:2rdj, PDBj:2rdj
• PDBsum: 2rdj
• PubMed: 18448122
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)