Structure of PDB 2d0b Chain A Binding Site BS01

Receptor Information

>2d0b Chain A (length=308) Species: 1422 (Geobacillus stearothermophilus)

SNYVIQADQQLLDALRAHYEGALSDRLPAGALFAVKRPDVVITAYRSGKV
LFQGKAAEQEAAKWISGASASNETADHQPSALAAHQLGSLSAIGSDEVGT
GDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAPAIMETVP
HAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIAPAEPEAIII
DEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLE
EMEQLSRAVGLLLPKGAGAIVDEAAARIIRARGEEMLETCAKLHFANTKK
ALAIAKRR

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: 2d0b Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2d0b Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): D97 E98 D202
• Binding residue (residue number reindexed from 1): D96 E97 D201
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.26.4: ribonuclease H.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006298 mismatch repair
• GO:0006401 RNA catabolic process
• GO:0016070 RNA metabolic process
• GO:0043137 DNA replication, removal of RNA primer

Cellular Component

• GO:0005737 cytoplasm
• GO:0032299 ribonuclease H2 complex

External links

• PDB: RCSB:2d0b, PDBe:2d0b, PDBj:2d0b
• PDBsum: 2d0b
• PubMed: 16343535
• UniProt: Q6L6Q4