Structure of PDB 8ooy Chain A

Receptor sequence

>8ooyA (length=604) Species: 866768 (Escherichia coli 'BL21-Gold(DE3)pLysS AG')

GPHDNYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFA
IEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYD
RGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFE
EIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLN
VFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIA
GEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLP
KVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDP
NLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLL
TAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLA
RQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLY
LPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRV
RMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENW
DQAH

3D structure

• PDB: 8ooy A four-point molecular handover during Okazaki maturation.
• Chain: A
• Resolution: 4.0 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	rna	A	S582 K584 K643 T664 T666 T672 D673 N675 Y766 M768 S769 F771 R775 Q776 R781 R841 Q849	S258 K260 K319 T340 T342 T348 D349 N351 Y442 M444 S445 F447 R451 Q452 R457 R517 Q525
BS02	rna	A	K479 T602 P603 G604 T609 S610 E611 K635 Y640 R668 N678 P680 V681 H881 D882	K155 T278 P279 G280 T285 S286 E287 K311 Y316 R344 N354 P356 V357 H557 D558
BS03	dna	A	R781 G833	R457 G509

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication

External links

• PDB: RCSB:8ooy, PDBe:8ooy, PDBj:8ooy
• PDBsum: 8ooy
• PubMed: 37620586
• UniProt: P00582|DPO1_ECOLI DNA polymerase I (Gene Name=polA)