Structure of PDB 6tfd Chain A Binding Site BS02

Receptor Information

>6tfd Chain A (length=423) Species: 670307 (Hyphomicrobium denitrificans 1NES1)

SHAPVVFTLRTGIAEGRMVYIGVGGDIDRQVNPKLVVHEGETVQINLING
EGAQHDAVIDQYAARSAIVSGKNASSTFSFIASKVGQFDYYCSLPGHRQA
GMQGVLQVVPGNRAEMPSTAADITRDPADLPGPIGARQAKTVRIDLETVE
LKGQLDDKTTYTYWTFNGKVPGPFLRVRVGDTVELHLKNAKDSLMIHSVD
FHGATGPGGAAAYTQTDPGAETVVTFKALVPGIFVYHCATPSVPNHITNG
MYGLLLVEPEGGLPQVDREFYVMQGEIYTVKPFGTSGEQEMDYEKLISEK
PEYFLFNGSVGALTRTHPLYANVGETVRIFFGVGGPNFTSSFHVIGEIFD
HVYALGSVTSPPLTGVQTVSVPPGGATIVDFKLDRGGRYVLVDHALSRLD
HGLVGFLNVDGPKNDAIMHEGPP

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: 6tfd Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tfd Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): H227 H262
• Binding residue (residue number reindexed from 1): H202 H237
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H222 D225 H227 H262 C263 H271 M276 H368 Q392 T393 H419
• Catalytic site (residue number reindexed from 1): H197 D200 H202 H237 C238 H246 M251 H343 Q367 T368 H394
• Enzyme Commision number: 1.7.2.1: nitrite reductase (NO-forming).

Gene Ontology

Molecular Function

• GO:0005507 copper ion binding
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050421 nitrite reductase (NO-forming) activity

External links

• PDB: RCSB:6tfd, PDBe:6tfd, PDBj:6tfd
• PDBsum: 6tfd
• PubMed: 32431838
• UniProt: N0B9M5