Structure of PDB 6vgm Chain D

Receptor sequence

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

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 6vgm Promutagenic bypass of 7,8-dihydro-8-oxoadenine by translesion synthesis DNA polymerase Dpo4.
• Chain: D
• Resolution: 2.84 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	E106 K152 G185 I186 G187 I189 T190 R298 R300 T301 K321	E106 K152 G185 I186 G187 I189 T190 R298 R300 T301 K321
BS02	dna	D	V32 S34 F37 S40 G41 A42 G58 P60 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 K275 L293 R331 R332 R336	V32 S34 F37 S40 G41 A42 G58 P60 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 K275 L293 R331 R332 R336
BS03	MG	D	D7 D105 E106	D7 D105 E106
BS04	1FZ	D	D7 F8 Y10 F11 Y12 A44 T45 Y48 R51 A57 D105 K159	D7 F8 Y10 F11 Y12 A44 T45 Y48 R51 A57 D105 K159
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:6vgm, PDBe:6vgm, PDBj:6vgm
• PDBsum: 6vgm
• PubMed: 32686822
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)