Structure of PDB 5d4i Chain A Binding Site BS04

Receptor Information
>5d4i Chain A (length=334) Species: 511 (Alcaligenes faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDA
GTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGA
LGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIM
VLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYED
TVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPH
LIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVN
HNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG
Ligand information
Ligand IDNO2
InChIInChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1
InChIKeyIOVCWXUNBOPUCH-UHFFFAOYSA-M
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341		[O-]N=O
OpenEye OEToolkits 1.5.0N(=O)[O-]
FormulaN O2
NameNITRITE ION
ChEMBL
DrugBankDB12529
ZINC
PDB chain5d4i Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5d4i Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H255 I257 H306
Binding residue
(residue number reindexed from 1)		H250 I252 H301
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H95 D98 H100 H135 C136 H145 M150 H255 E279 T280 H306
Catalytic site (residue number reindexed from 1) H90 D93 H95 H130 C131 H140 M145 H250 E274 T275 H301
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5d4i, PDBe:5d4i, PDBj:5d4i
PDBsum5d4i
PubMed26929369
UniProtP38501|NIR_ALCFA Copper-containing nitrite reductase (Gene Name=nirK)

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