Structure of PDB 1aom Chain A Binding Site BS01

Receptor Information
>1aom Chain A (length=439) Species: 82367 (Paracoccus pantotrophus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDPAAPPEFGMKEMRESWKVHVAPEDRPTQQMNDWDLENLFSVTLRDAGQ
IALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMK
EPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEP
KKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYT
DLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVA
IEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNA
WKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAM
TGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQE
SALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY
Ligand information
Ligand IDDHE
InChIInChI=1S/C34H34N4O10.Fe/c1-15-17(5-7-27(39)40)21-10-22-18(6-8-28(41)42)16(2)20(36-22)11-25-33(3,13-29(43)44)32(48)24(38-25)12-26-34(4,14-30(45)46)31(47)23(37-26)9-19(15)35-21;/h9-12H,5-8,13-14H2,1-4H3,(H6,35,36,37,38,39,40,41,42,43,44,45,46,47,48);/q;+2/p-2/t33-,34-;/m1./s1
InChIKeyXLQCGNUTSJTZNF-YDXXJHAFSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(C6=O)(C)CC(=O)O)C(=O)C(C8=C2)(C)CC(=O)O)C)CCC(=O)O
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7[C@@](C6=O)(C)CC(=O)O)C(=O)[C@](C8=C2)(C)CC(=O)O)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N@]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C@@](C)(CC(O)=O)C6=O)[C@@](C)(CC(O)=O)C5=O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C](C)(CC(O)=O)C6=O)[C](C)(CC(O)=O)C5=O
FormulaC34 H32 Fe N4 O10
NameHEME D
ChEMBL
DrugBank
ZINC
PDB chain1aom Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1aom Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		R174 H200 I201 R216 R243 S244 Y263 A301 A302 H345 R391 F444 W522 F557
Binding residue
(residue number reindexed from 1)		R46 H72 I73 R88 R115 S116 Y135 A173 A174 H217 R263 F316 W394 F429
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H345 H388
Catalytic site (residue number reindexed from 1) H217 H260
Enzyme Commision number 1.7.2.1: nitrite reductase (NO-forming).
1.7.99.1: hydroxylamine reductase.
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0050418 hydroxylamine reductase activity
GO:0050421 nitrite reductase (NO-forming) activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1aom, PDBe:1aom, PDBj:1aom
PDBsum1aom
PubMed9311786
UniProtP72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

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