Structure of PDB 5d4h Chain A

Receptor sequence

>5d4hA (length=337) Species: 511 (Alcaligenes faecalis)

ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVID
DAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAAT
GALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGA
IMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAY
EDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTR
PHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAY
VNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT

3D structure

• PDB: 5d4h Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
• Chain: A
• Resolution: 1.3 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): H92 D95 H97 H132 C133 H142 M147 H252 E276 T277 H303
• 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	H92 C133 H142 M147
BS02	CU	A	H100 H135	H97 H132
BS03	NO2	A	D98 H100 H135	D95 H97 H132
BS04	NO2	A	H255 I257 H306	H252 I254 H303

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:5d4h, PDBe:5d4h, PDBj:5d4h
• PDBsum: 5d4h
• PubMed: 26929369
• UniProt: P38501|NIR_ALCFA Copper-containing nitrite reductase (Gene Name=nirK)