Structure of PDB 5of5 Chain A

Receptor sequence

>5of5A (length=334) Species: 223 (Achromobacter cycloclastes)

VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREG
TEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGAL
GGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMV
LPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDA
VKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHL
IGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNH
NLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

3D structure

• PDB: 5of5 Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.
• Chain: A
• Resolution: 1.08 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): H89 D92 H94 H129 C130 H139 M144 H249 E273 T274 H300
• 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	H89 C130 H139 M144
BS02	CU	A	H100 H135	H94 H129
BS03	NO2	A	D98 H100 H135	D92 H94 H129
BS04	NO2	A	V68 P69 N151 G179 E180 Q181	V62 P63 N145 G173 E174 Q175
BS05	NO2	A	G324 E325	G318 E319
BS06	NO2	A	P88 D89	P82 D83
BS07	NO2	A	V335 K336	V329 K330
BS08	NO2	A	D18 L19 T42 N65	D12 L13 T36 N59

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:5of5, PDBe:5of5, PDBj:5of5
• PDBsum: 5of5
• PubMed: 29755744
• UniProt: P25006|NIR_ACHCY Copper-containing nitrite reductase (Gene Name=nirK)