Structure of PDB 6vg6 Chain D

Receptor sequence

>6vg6D (length=341) Species: 2287 (Saccharolobus solfataricus)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 6vg6 Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4.
• Chain: D
• Resolution: 3.08 Å

Enzymatic activity

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	D	S103 D105 E106 K152 P184 G185 I186 G187 I189 T190 S297 R298 G299 T301	S103 D105 E106 K152 P184 G185 I186 G187 I189 T190 S297 R298 G299 T301
BS02	dna	D	V32 S34 S40 G41 A42 P60 G218 E219 A220 R242 K243 S244 G246 R247 I248 V249 T250 R331 R332 R336	V32 S34 S40 G41 A42 P60 G218 E219 A220 R242 K243 S244 G246 R247 I248 V249 T250 R331 R332 R336
BS03	XG4	D	Y10 Y12 T45 Y48 R51 M76 D105	Y10 Y12 T45 Y48 R51 M76 D105
BS04	MG	D	D7 D105 E106	D7 D105 E106
BS05	MG	D	D7 F8 D105	D7 F8 D105

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:6vg6, PDBe:6vg6, PDBj:6vg6
• PDBsum: 6vg6
• PubMed: 32686822
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)