Structure of PDB 2rdj Chain A

Receptor sequence

>2rdjA (length=341) Species: 273057 (Saccharolobus solfataricus P2)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 2rdj Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
• Chain: A
• Resolution: 2.2 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	A	D105 E106 K152 G185 G187 I189 T190 V296 S297 R298 T301	D105 E106 K152 G185 G187 I189 T190 V296 S297 R298 T301
BS02	dna	A	V32 S40 G41 A42 P60 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 L293 R331 R332 R336	V32 S40 G41 A42 P60 E219 A220 R242 K243 S244 I245 G246 R247 I248 T250 L293 R331 R332 R336
BS03	CA	A	D7 F8 D105	D7 F8 D105
BS04	CA	A	A181 I186	A181 I186
BS05	TMP	A	Y10 F11 Y12 A44 T45 R51 A57	Y10 F11 Y12 A44 T45 R51 A57

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)