Structure of PDB 4b5i Chain A Binding Site BS04

Receptor Information

>4b5i Chain A (length=256) Species: 487 (Neisseria meningitidis)

MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKN
PHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQIGMGIEEFDREGRFVRCDF
GRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDW
NIAHQNIDLKNWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVP
GYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPL
VVEYDY

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: 4b5i Chain A Residue 1257

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4b5i Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
• Resolution: 2.555 Å
• Binding residue (original residue number in PDB): N10 E36 D246 H247
• Binding residue (residue number reindexed from 1): N10 E36 D246 H247
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N8 N10 E36 Y109 D149 N151 D221 D246 H247
• Catalytic site (residue number reindexed from 1): N8 N10 E36 Y109 D149 N151 D221 D246 H247
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:4b5i, PDBe:4b5i, PDBj:4b5i
• PDBsum: 4b5i
• PubMed: 23035246
• UniProt: Q7DD47