Structure of PDB 2vm3 Chain A Binding Site BS03

Receptor Information

>2vm3 Chain A (length=333) Species: 85698 (Achromobacter xylosoxidans)

ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTT
LQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGG
AKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLP
RDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQ
VMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIG
GHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNL
IEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 2vm3 Chain A Residue 888

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vm3 Crystallography with Online Optical and X-Ray Absorption Spectroscopies Demonstrates an Ordered Mechanism in Copper Nitrite Reductase.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H165 D167
• Binding residue (residue number reindexed from 1): H163 D165
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H89 D92 H94 H129 C130 H139 M144 H249 E273 T274 H300
• Catalytic site (residue number reindexed from 1): H87 D90 H92 H127 C128 H137 M142 H247 E271 T272 H298
• Enzyme Commision number: 1.7.2.1: nitrite reductase (NO-forming).

Gene Ontology

Molecular Function

• GO:0005507 copper ion binding
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050421 nitrite reductase (NO-forming) activity

Biological Process

• GO:0019333 denitrification pathway
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:2vm3, PDBe:2vm3, PDBj:2vm3
• PDBsum: 2vm3
• PubMed: 18353369
• UniProt: O68601