Structure of PDB 5d4i Chain A

Receptor sequence

>5d4iA (length=334) Species: 511 (Alcaligenes faecalis)

AAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDA
GTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGA
LGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIM
VLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYED
TVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPH
LIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVN
HNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG

3D structure

• PDB: 5d4i Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
• Chain: A
• Resolution: 1.6 Å

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).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	CU	A	H95 C136 H145 M150	H90 C131 H140 M145
BS02	CU	A	H100 H135	H95 H130
BS03	NO2	A	D98 H100 H135	D93 H95 H130
BS04	NO2	A	H255 I257 H306	H250 I252 H301

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:5d4i, PDBe:5d4i, PDBj:5d4i
• PDBsum: 5d4i
• PubMed: 26929369
• UniProt: P38501|NIR_ALCFA Copper-containing nitrite reductase (Gene Name=nirK)