Structure of PDB 8rfp Chain A Binding Site BS04

Receptor Information

>8rfp Chain A (length=334) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DLKLPRQKVELVAPPFVHAHEQATKQGPKIVEFKLTIEEKKVVIDEKGTT
FQAMTFNGSMPGPLMVVHEGDYVETTLVNPATNTMPHNIDFHSATGALGG
GALTLINPGEQVVLRWKATKTGVFVYHCAPGGPMIPWHVVSGMNGAVMVL
PRDGLNDGKGHALKYDKVYYVGEQDMYVPRDEKGNFKSYDSPGEAFTDTE
EMMKKLIPSHVVFNGKVGALTGKNALTANVGENVLIVHSQANRDSRPHLI
GGHGDYVWETGKFGNAPEVGLETWFIRGGSAGAAMYKFMQPGIYAYVTHN
LIEAADLCATAHFKVEGKWNDDLMTQVKAPAEIP

Ligand information

Ligand ID

NO2

InChI

InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1

InChIKey

IOVCWXUNBOPUCH-UHFFFAOYSA-M

SMILES

Software	SMILES
ACDLabs 10.04 CACTVS 3.341	[O-]N=O
OpenEye OEToolkits 1.5.0	N(=O)[O-]

Formula

N O2

Name

NITRITE ION

PDB chain

8rfp Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8rfp Spectroscopically validated pH-dependent MSOX movies provide detailed mechanism of copper nitrite reductases.
Resolution	1.23 Å
Binding residue (original residue number in PDB)	D92 H94 H129
Binding residue (residue number reindexed from 1)	D90 H92 H127
Annotation score	5

Gene Ontology

	Molecular Function
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

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Molecular Function

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Cellular Component

External links

PDB	RCSB:8rfp, PDBe:8rfp, PDBj:8rfp
PDBsum	8rfp
PubMed	39002715
UniProt	Q89EJ6

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