Structure of PDB 4nid Chain A Binding Site BS03

Receptor Information

>4nid Chain A (length=203) Species: 562 (Escherichia coli)

QEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAM
TNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPD
FQPDACLINRYAPGAKLCLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKR
NDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQ
AGK

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 4nid Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4nid Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.
• Resolution: 1.58 Å
• Binding residue (original residue number in PDB): H131 D133 H187
• Binding residue (residue number reindexed from 1): H120 D122 H176
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.33: DNA oxidative demethylase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008198 ferrous iron binding
• GO:0035515 oxidative RNA demethylase activity
• GO:0035516 broad specificity oxidative DNA demethylase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0006281 DNA repair
• GO:0006307 DNA alkylation repair
• GO:0035513 oxidative RNA demethylation
• GO:0042245 RNA repair
• GO:0070989 oxidative demethylation
• GO:0072702 response to methyl methanesulfonate

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4nid, PDBe:4nid, PDBj:4nid
• PDBsum: 4nid
• PubMed: 24596302
• UniProt: P05050|ALKB_ECOLI Alpha-ketoglutarate-dependent dioxygenase AlkB (Gene Name=alkB)