Structure of PDB 5og3 Chain A

Receptor sequence

>5og3A (length=332) Species: 223 (Achromobacter cycloclastes)

DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGT
EIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALG
GGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVL
PRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAV
KAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLI
GGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHN
LIEAFELGAAGHFKVTGEWNDDLMTSVVKPAS

3D structure

• PDB: 5og3 Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.
• Chain: A
• Resolution: 1.7 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	R250 D251	R243 D244
BS04	NO2	A	D251 R253 E310	D244 R246 E303
BS05	NO2	A	G117 E118	G110 E111
BS06	NO2	A	W265 T267 G268 K269	W258 T260 G261 K262
BS07	NO2	A	E47 K48 H60	E40 K41 H53
BS08	NO2	A	D98 H100 H135	D91 H93 H128
BS09	NO	A	D98 H135	D91 H128

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:5og3, PDBe:5og3, PDBj:5og3
• PDBsum: 5og3
• PubMed: 29755744
• UniProt: P25006|NIR_ACHCY Copper-containing nitrite reductase (Gene Name=nirK)