Structure of PDB 6zav Chain A Binding Site BS06

Receptor Information

>6zav Chain A (length=345) Species: 566679 (Bradyrhizobium sp. ORS 375)

DLKLPRQRVDLVAPPFVHVHEQATKQGPKIMEFKLVVQEKKMVIDEKGTT
FQAMTFNGSMPGPLMVVHEGDYVEVTLVNPATNTMPHNIDFHSATGALGG
GALTLINPGEQVVLRWKATRTGVFVYHCAPGGPMIPWHVVSGMNGAVMVL
PRDGLNDGHGHSLRYDRIYYIGEQDLYVPRDEKGNFKSYDSPGEAYSDTE
EVMRKLTPTHVVFNGKAGALTGKNALNANVGENVLIVHSQANRDSRPHLI
GGHGDYVWETGKFSNAPETGLETWFIRGGSAGAALYKFLQPGIYAYVTHN
LIEAANLGATAHFKVEGKWNDDLMTQVKAPADIPTGSTNENLYFQ

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: 6zav Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zav An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
• Resolution: 1.19 Å
• Binding residue (original residue number in PDB): H94 H129
• Binding residue (residue number reindexed from 1): H92 H127
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H89 D92 H94 H129 C130 H140 M145 H250 E274 T275 H301
• Catalytic site (residue number reindexed from 1): H87 D90 H92 H127 C128 H138 M143 H248 E272 T273 H299
• 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: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:6zav, PDBe:6zav, PDBj:6zav
• PDBsum: 6zav
• PubMed: 33523860
• UniProt: H0SLX7