Structure of PDB 3d1i Chain A

Receptor sequence

>3d1iA (length=519) Species: 186931 (Thioalkalivibrio nitratireducens)

NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMG
ERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLI
AGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRG
AWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHE
AAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGL
GTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYN
CNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGA
ALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPR
DMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPV
AKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSI
SKSKEAVSLLNDAIDAQVA

3D structure

• PDB: 3d1i High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens
• Chain: A
• Resolution: 1.8 Å

Enzymatic activity

• Enzyme Commision number: 1.7.2.2: nitrite reductase (cytochrome; ammonia-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	HEC	A	H113 A114 D125 H126 V129 R131 C184 C187 K188 C299 H300 Y303 C305 F327 H361 N486	H109 A110 D121 H122 V125 R127 C180 C183 K184 C295 H296 Y299 C301 F323 H357 N482
BS02	HEC	A	H70 Q73 L225 C227 C230 H231 A290 M295 M384 Y395 T396 H398	H66 Q69 L221 C223 C226 H227 A286 M291 M380 Y391 T392 H394
BS03	HEC	A	S84 P116 R117 H119 F121 M122 D125 C187 L225 M229 C296 C299 H300	S80 P112 R113 H115 F117 M118 D121 C183 L221 M225 C292 C295 H296
BS04	HEC	A	H300 E363 F367 H372 A378 C379 C382 H383 T402 P403 R404 I427 K431 N486 F490 H491	H296 E359 F363 H368 A374 C375 C378 H379 T398 P399 R400 I423 K427 N482 F486 H487
BS05	HEC	A	V371 H372 N375 P403 A410 C411 C414 H415 W418 I427 F490	V367 H368 N371 P399 A406 C407 C410 H411 W414 I423 F486
BS06	HEC	A	C14 F15 H18 I21 H25 C35 C38 H39 T59 I193 L194 F228 P233 H234 R239 F274 R276 R282	C10 F11 H14 I17 H21 C31 C34 H35 T55 I189 L190 F224 P229 H230 R235 F270 R272 R278
BS07	HEC	A	K29 H30 V33 H37 C66 C69 H70 H231 A236	K25 H26 V29 H33 C62 C65 H66 H227 A232
BS08	HEC	A	C14 C17 H18 H39 A41 H44 V45 A48 S49 S50 R52 M53 R56 P57 R276 G277	C10 C13 H14 H35 A37 H40 V41 A44 S45 S46 R48 M49 R52 P53 R272 G273
BS09	CA	A	E302 Y303 K358 Q360	E298 Y299 K354 Q356
BS10	CA	A	S84 P116	S80 P112
BS11	NO2	A	Y303 H361	Y299 H357

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding
• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
• GO:0046872 metal ion binding

Biological Process

• GO:0019645 anaerobic electron transport chain
• GO:0042128 nitrate assimilation
• GO:0097164 ammonium ion metabolic process

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space
• GO:0042597 periplasmic space

External links

• PDB: RCSB:3d1i, PDBe:3d1i, PDBj:3d1i
• PDBsum: 3d1i
• PubMed: 19393666
• UniProt: L0DSL2|NIR_THIND Cytochrome c-552 (Gene Name=nir)