Structure of PDB 2nqj Chain A

Receptor sequence

>2nqjA (length=279) Species: 562 (Escherichia coli)

MKYIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTID
EFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQ
LGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQ
GSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTF
ADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQD
DRFDGIPLILQTINPDIWAEEIAWLKAQQ

3D structure

• PDB: 2nqj DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
• Chain: A
• Resolution: 2.45 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.2: deoxyribonuclease IV.

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	H7 S9 A10 A11 G12 F32 N35 Q36 R37 Y72 H109 D229 R230 H231 Q261	H7 S9 A10 A11 G12 F32 N35 Q36 R37 Y72 H109 D229 R230 H231 Q261	PDBbind-CN: Kd=114nM
BS02	dna	A	N35 R37 Q38 W39 L73 L114 Q150 G151 S152 V228	N35 R37 Q38 W39 L73 L114 Q150 G151 S152 V228	PDBbind-CN: Kd=114nM
BS03	ZN	A	H69 H109 E145	H69 H109 E145
BS04	ZN	A	E145 D179 H216 Q261	E145 D179 H216 Q261
BS05	ZN	A	H182 D229 H231	H182 D229 H231

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008270 zinc ion binding
• GO:0008296 3'-5'-DNA exonuclease activity
• GO:0008833 deoxyribonuclease IV (phage-T4-induced) activity
• GO:0016791 phosphatase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:2nqj, PDBe:2nqj, PDBj:2nqj
• PDBsum: 2nqj
• PubMed: 18408731
• UniProt: P0A6C1|END4_ECOLI Endonuclease 4 (Gene Name=nfo)