Structure of PDB 5i6m Chain A

Receptor sequence

>5i6mA (length=332) Species: 223 (Achromobacter cycloclastes)

DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGT
EIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALG
GGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVL
PRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAV
KAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLI
GGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHN
LIEAFELGAAGHFKVTGEWNDDLMTSVVKPAS

3D structure

• PDB: 5i6m Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.
• Chain: A
• Resolution: 1.09 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): H88 D91 H93 H128 C129 H138 M143 H248 E272 T273 H299
• 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	H88 C129 H138 M143
BS02	CU	A	H100 H135	H93 H128
BS03	NO2	A	D98 H100 H135	D91 H93 H128
BS04	NO	A	D98 H100 H135	D91 H93 H128
BS05	NO2	A	R250 D251	R243 D244
BS06	NO2	A	R253 N307 E310	R246 N300 E303
BS07	NO2	A	G225 A226 T228 H231	G218 A219 T221 H224

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:5i6m, PDBe:5i6m, PDBj:5i6m
• PDBsum: 5i6m
• PubMed: 27437114
• UniProt: P25006|NIR_ACHCY Copper-containing nitrite reductase (Gene Name=nirK)