Structure of PDB 6vgm Chain A Binding Site BS02

Receptor Information

>6vgm Chain A (length=341) Species: 2287 (Saccharolobus solfataricus)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

Ligand information

>6vgm Chain T (length=16)

atagaatccttccccc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vgm Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4.
• Resolution: 2.84 Å
• Binding residue (original residue number in PDB): V32 S34 S40 G41 A42 G58 I59 P60 E219 A220 R240 K243 S244 I245 G246 R247 I248 T250 R331 R332
• Binding residue (residue number reindexed from 1): V32 S34 S40 G41 A42 G58 I59 P60 E219 A220 R240 K243 S244 I245 G246 R247 I248 T250 R331 R332

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:6vgm, PDBe:6vgm, PDBj:6vgm
• PDBsum: 6vgm
• PubMed: 32686822
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)