Structure of PDB 5i6k Chain A

Receptor sequence

>5i6kA (length=334) Species: 223 (Achromobacter cycloclastes)

VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREG
TEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGAL
GGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMV
LPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDA
VKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHL
IGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNH
NLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM

3D structure

• PDB: 5i6k Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.
• Chain: A
• Resolution: 1.07 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	W265 T267 G268 K269 N272	W259 T261 G262 K263 N266
BS05	NO2	A	R250 D251	R244 D245

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:5i6k, PDBe:5i6k, PDBj:5i6k
• PDBsum: 5i6k
• PubMed: 27437114
• UniProt: P25006|NIR_ACHCY Copper-containing nitrite reductase (Gene Name=nirK)