Structure of PDB 3w52 Chain A

Receptor sequence

>3w52A (length=256) Species: 3702 (Arabidopsis thaliana)

WGKEGHEIICKIAQTRLDETAAKAVKELLPESAEGDLSSLCLWADRVKFR
YHWSSPLHYINTPDACSYQYNRDCKDESGEKGRCVAGAIYNYTTQLLSYK
QYNLTEALLFVSHFMGDIHQPLHVSYASDKGGNTIEVHWYTRKANLHHIW
DSNIIETAEADLYNSALEGMVDALKKNITTEWADQVKRWETCTKKTACPD
IYASEGIQAACDWAYKGVTEGDTLEDEYFYSRLPIVYQRLAQGGVRLAAT
LNRIFG

3D structure

• PDB: 3w52 Mechanistic insights to catalysis by a zinc-dependent bi-functional nuclease from Arabidopsis thaliana
• Chain: A
• Resolution: 1.76 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): W1 H6 D45 K48 H58 H120 D124 H130 H154 D158
• Catalytic site (residue number reindexed from 1): W1 H6 D45 K48 H58 H113 D117 H123 H147 D151
• Enzyme Commision number: 3.1.30.1: Aspergillus nuclease S1.

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	ADE	A	Y59 K137 H154	Y59 K130 H147
BS02	ZN	A	D45 H58 H120 D124	D45 H58 H113 D117
BS03	ZN	A	H130 H154 D158	H123 H147 D151
BS04	ZN	A	W1 H6 D124	W1 H6 D117

Gene Ontology

Molecular Function

• GO:0000014 single-stranded DNA endodeoxyribonuclease activity
• GO:0003676 nucleic acid binding
• GO:0004519 endonuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0043765 T/G mismatch-specific endonuclease activity
• GO:0046872 metal ion binding
• GO:1990238 double-stranded DNA endonuclease activity

Biological Process

• GO:0006308 DNA catabolic process

External links

• PDB: RCSB:3w52, PDBe:3w52, PDBj:3w52
• PDBsum: 3w52
• UniProt: Q9C9G4|ENDO2_ARATH Endonuclease 2 (Gene Name=ENDO2)