Structure of PDB 1rdd Chain A Binding Site BS01

Receptor Information

>1rdd Chain A (length=155) Species: 562 (Escherichia coli)

MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELM
AAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKN
VDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTG
YQVEV

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 1rdd Chain A Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rdd Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): D10 G11 E48
• Binding residue (residue number reindexed from 1): D10 G11 E48
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D10 G11 E48 D70 H124 D134
• Catalytic site (residue number reindexed from 1): D10 G11 E48 D70 H124 D134
• Enzyme Commision number: 3.1.26.4: ribonuclease H.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003676 nucleic acid binding
• GO:0004519 endonuclease activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity
• GO:0005515 protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006401 RNA catabolic process
• GO:0043137 DNA replication, removal of RNA primer

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:1rdd, PDBe:1rdd, PDBj:1rdd
• PDBsum: 1rdd
• PubMed: 8108376
• UniProt: P0A7Y4|RNH_ECOLI Ribonuclease HI (Gene Name=rnhA)