Structure of PDB 1stx Chain B

Receptor sequence

>1stxB (length=244) Species: 562 (Escherichia coli)

SLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTAVLSTIFELFSRPI
INKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENE
KIKFTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTY
NINELNEIPKPYKGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVE
GKGIFDSEDEFLDYWRNYERTSQLRNDKYNNISEYRNWIYRGRK

3D structure

• PDB: 1stx DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.4: type II site-specific deoxyribonuclease.

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	B	L180 S183 G184 N185 T222 S223	L179 S182 G183 N184 T221 S222
BS02	dna	B	Q69 H71	Q68 H70
BS03	dna	B	N70 G109 T111 S112 K119 N120	N69 G108 T110 S111 K118 N119
BS04	dna	B	T37 E45 D74 K92 T93 T94 Y95 T106 S183 T186 N188	T36 E44 D73 K91 T92 T93 Y94 T105 S182 T185 N187
BS05	MN	B	E45 D74 I91	E44 D73 I90
BS06	MN	B	Q68 H71	Q67 H70

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0004519 endonuclease activity
• GO:0009036 type II site-specific deoxyribonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009307 DNA restriction-modification system

External links

• PDB: RCSB:1stx, PDBe:1stx, PDBj:1stx
• PDBsum: 1stx
• PubMed: 15170321
• UniProt: P04390|T2E5_ECOLX Type II restriction enzyme EcoRV (Gene Name=ecoRVR)