Structure of PDB 2agp Chain B

Receptor sequence

>2agpB (length=341) Species: 2287 (Saccharolobus solfataricus)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 2agp Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.
• Chain: B
• Resolution: 2.9 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	B	L19 E79 V80 Q83 R87	L19 E79 V80 Q83 R87
BS02	dna	B	R87 K135	R87 K135
BS03	dna	B	G185 G187 I189 T190 R298 G299 R300 T301 K339	G185 G187 I189 T190 R298 G299 R300 T301 K339
BS04	dna	B	F37 S40 G41 K221 R242 K243 S244 G246 R247 L293 R331 R332 R336	F37 S40 G41 K221 R242 K243 S244 G246 R247 L293 R331 R332 R336
BS05	CA	B	D7 F8 D105	D7 F8 D105
BS06	MG	B	D105 E106	D105 E106
BS07	DGT	B	D7 Y10 Y12 A44 T45 R51 D105 K159	D7 Y10 Y12 A44 T45 R51 D105 K159

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:2agp, PDBe:2agp, PDBj:2agp
• PDBsum: 2agp
• PubMed: 16107880
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)