Structure of PDB 1d9d Chain A

Receptor sequence

>1d9dA (length=601) Species: 562 (Escherichia coli)

MISYDNYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSF
AIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKY
DRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITF
EEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPL
NVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEI
AGEEFNLSSTKQLQTILFEKQGIKPLKKTPSTSEEVLEELALDYPLPKVI
LEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQ
NIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAF
AEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQL
NIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPD
IKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMI
MQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQA
H

3D structure

• PDB: 1d9d Structural origins of the exonuclease resistance of a zwitterionic RNA.
• Chain: A
• Resolution: 2.18 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	D355 E357 T358 D359 S360 L361 Q419 K422 Y423 D424 D457 M458 D459 T470 I471 F473 T485 Y497 D501 S658 Y659 H660	D32 E34 T35 D36 S37 L38 Q96 K99 Y100 D101 D134 M135 D136 T147 I148 F150 T162 Y174 D178 S331 Y332 H333
BS02	ZN	A	D355 E357 D501	D32 E34 D178
BS03	ZN	A	H901 E905	H574 E578
BS04	MG	A	L723 N761 Y791	L396 N434 Y464

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:1d9d, PDBe:1d9d, PDBj:1d9d
• PDBsum: 1d9d
• PubMed: 10588690
• UniProt: P00582|DPO1_ECOLI DNA polymerase I (Gene Name=polA)