Structure of PDB 2dv6 Chain D Binding Site BS02

Receptor Information

>2dv6 Chain D (length=422) Species: 53399 (Hyphomicrobium denitrificans)

HAPVVFTLRTGIAEGRMVYIGVGGDIDHKINPTLVVHEGETVQVNLVNGE
GAQHDVVVDQYAARSAIVNGKNASSTFSFVASKVGEFNYYCSIAGHRQAG
MEGNIQVLPGNRAEMKSSGADITRDPADLPGPIGPRQAKTVRIDLETVEV
KGQLDDNTTYTYWTFNGKVPGPFLRVRVGDTVELHLKNHKDSLMVHSVDF
HGATGPGGAAAFTQTDPGEETVVTFKALIPGIYVYHCATPSVPTHITNGM
YGLLLVEPEGGLPQVDREFYVMQGEIYTVKSFGTSGEQEMDYEKLINEKP
EYFLFNGSVGSLTRSHPLYASVGETVRIFFGVGGPNFTSSFHVIGEIFDH
VYSLGSVVSPPLIGVQTVSVPPGGATIVDFKIDRAGRYILVDHALSRLEH
GLVGFLNVDGPKNDSIMHEGPA

Ligand information

• Ligand ID: CU
• InChI: InChI=1S/Cu/q+2
• InChIKey: JPVYNHNXODAKFH-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Cu+2]
  CACTVS 3.341: [Cu++]
• Formula: Cu
• Name: COPPER (II) ION
• DrugBank: DB14552
• PDB chain: 2dv6 Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dv6 Structure and function of a hexameric copper-containing nitrite reductase.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): H224 H259
• Binding residue (residue number reindexed from 1): H201 H236
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H219 D222 H224 H259 C260 H268 M273 H365 Q389 T390 H416
• Catalytic site (residue number reindexed from 1): H196 D199 H201 H236 C237 H245 M250 H342 Q366 T367 H393
• Enzyme Commision number: 1.7.2.1: nitrite reductase (NO-forming).

Gene Ontology

Molecular Function

• GO:0005507 copper ion binding
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0050421 nitrite reductase (NO-forming) activity

External links

• PDB: RCSB:2dv6, PDBe:2dv6, PDBj:2dv6
• PDBsum: 2dv6
• PubMed: 17360521
• UniProt: Q8KKH4