Structure of PDB 8pdy Chain J Binding Site BS04

Receptor Information

>8pdy Chain J (length=1355) Species: 562 (Escherichia coli)

KTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIF
GPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTA
HIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTE
EQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSET
KRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFAT
SDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRR
GRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLR
LHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL
DEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFD
GDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGE
LVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRIL
GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVA
EIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQ
EEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITAN
FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED
DCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNT
LLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG
EAIGVIAAQSIGEPGTQLTMRTFHAAAESSIQVKNKGSIKLSNVKSVVNS
SGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVAN
WDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTA
GGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGD
TLARIPQESKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGK
RRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILR
LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSS
DFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISA
ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRR
RAAGE

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 8pdy Chain J Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pdy Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): C72 C85
• Binding residue (residue number reindexed from 1): C60 C73
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006352 DNA-templated transcription initiation
• GO:0006879 intracellular iron ion homeostasis
• GO:0009408 response to heat
• GO:0031564 transcription antitermination
• GO:0032784 regulation of DNA-templated transcription elongation
• GO:0036460 cellular response to cell envelope stress
• GO:0042128 nitrate assimilation
• GO:0044780 bacterial-type flagellum assembly
• GO:0046677 response to antibiotic
• GO:0048870 cell motility
• GO:0071973 bacterial-type flagellum-dependent cell motility
• GO:0090605 submerged biofilm formation
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0000345 cytosolic DNA-directed RNA polymerase complex
• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0008023 transcription elongation factor complex
• GO:0016020 membrane

External links

• PDB: RCSB:8pdy, PDBe:8pdy, PDBj:8pdy
• PDBsum: 8pdy
• PubMed: 38589445
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)