Structure of PDB 2jim Chain A

Receptor sequence

>2jimA (length=720) Species: 876 (Desulfovibrio desulfuricans)

RPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGNPNNHNAGLLCLKGSLL
IPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPNS
VAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSFG
KDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIVA
DPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVNF
MDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAATM
SLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGGV
RDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFEA
LGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTLE
YADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFAR
RAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWPC
PSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAAE
EPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAART
GIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLDA
TDPVSREPEYKICAARVRKA

3D structure

• PDB: 2jim Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
• Chain: A
• Resolution: 2.45 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K49 S109 C140 M141 A180 M308 T344 G345 Q346
• Catalytic site (residue number reindexed from 1): K46 S106 C137 M138 A177 M305 T341 G342 Q343
• Enzyme Commision number: 1.9.6.1: nitrate reductase (cytochrome).

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	SF4	A	C13 C16 T18 C20 L46 C47 V183	C10 C13 T15 C17 L43 C44 V180
BS02	MGD	A	R14 Q111 C140 Q312 Q346 E416 T417 N418 T422 I443 E444 A445 P461 F463 S615 R617 H623 T624 T626 F689 N697 Y713	R11 Q108 C137 Q309 Q343 E413 T414 N415 T419 I440 E441 A442 P458 F460 S612 R614 H620 T621 T623 F686 N694 Y710
BS03	MGD	A	K49 G174 S175 N176 E179 A180 D204 P205 R206 D225 C307 M308 G309 R313 G345 Q346 M616 R617 V618 I619 W622 H623 K714	K46 G171 S172 N173 E176 A177 D201 P202 R203 D222 C304 M305 G306 R310 G342 Q343 M613 R614 V615 I616 W619 H620 K711

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0008940 nitrate reductase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0050140 nitrate reductase (cytochrome) activity
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006777 Mo-molybdopterin cofactor biosynthetic process
• GO:0042128 nitrate assimilation

Cellular Component

• GO:0042597 periplasmic space

External links

• PDB: RCSB:2jim, PDBe:2jim, PDBj:2jim
• PDBsum: 2jim
• PubMed: 18327621
• UniProt: P81186|NAPA_DESDA Periplasmic nitrate reductase (Gene Name=napA)