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Structure of PDB 1e2r Chain A Binding Site BS01

Receptor Information

>1e2r Chain A (length=532) Species: 266 (Paracoccus denitrificans)

DVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDL
TRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPP
EFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGS
TYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAE
IKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTR
GMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKT
TEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQ
TPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSF
PALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDP
EFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVD
DKTLELKHVIKDERLVTPTGKFNVYNTMTDTY

Ligand information

• Ligand ID: HEC
• InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
• InChIKey: HXQIYSLZKNYNMH-LJNAALQVSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
  OpenEye OEToolkits 1.5.0: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
  CACTVS 3.341: C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
  CACTVS 3.341: CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
• Formula: C34 H34 Fe N4 O4
• Name: HEME C
• PDB chain: 1e2r Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1e2r X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus.
• Resolution: 1.59 Å
• Binding residue (original residue number in PDB): C65 C68 H69 G78 L81 Y93 F97 S102 A104 M106 P107 W109
• Binding residue (residue number reindexed from 1): C30 C33 H34 G43 L46 Y58 F62 S67 A69 M71 P72 W74
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C65 C68 H69 M106 H345 H388
• Catalytic site (residue number reindexed from 1): C30 C33 H34 M71 H310 H353
• 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

External links

• PDB: RCSB:1e2r, PDBe:1e2r, PDBj:1e2r
• PDBsum: 1e2r
• PubMed: 10827177
• UniProt: P72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

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