Structure of PDB 4rzr Chain D

Receptor sequence

>4rzrD (length=342) Species: 273057 (Saccharolobus solfataricus P2)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE

3D structure

• PDB: 4rzr Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.
• Chain: D
• 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	D	V32 F33 S34 G41 A42 V62 E63 M76 K78 G218 R242 K243 S244 I245 G246 R247 T250 L293 R332 R336	V32 F33 S34 G41 A42 V62 E63 M76 K78 G218 R242 K243 S244 I245 G246 R247 T250 L293 R332 R336
BS02	dna	D	K152 P184 G185 G187 I189 T190 K193 S297 R298 G299	K152 P184 G185 G187 I189 T190 K193 S297 R298 G299
BS03	DCP	D	Y10 F11 Y12 A44 T45 Y48 R51 D105 K159	Y10 F11 Y12 A44 T45 Y48 R51 D105 K159
BS04	CA	D	D7 F8 D105	D7 F8 D105
BS05	CA	D	D7 D105 E106	D7 D105 E106

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:4rzr, PDBe:4rzr, PDBj:4rzr
• PDBsum: 4rzr
• PubMed: 26327169
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)