Structure of PDB 4jk2 Chain I Binding Site BS02

Receptor Information
>4jk2 Chain I (length=1160) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLF
CARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIEL
ASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ
QILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE
TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDG
GRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL
DNGRRGRAITGSNKRPLKSLADMIKGGKRVDYSGRSVITVGPYLRLHQCG
LPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIR
EHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMA
VHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDC
VNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKT
SLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPT
VIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQ
FQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQV
SFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGL
NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTH
EGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQ
WCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGV
IAAQSIGEPGTQLTMRDITGGLPRVADLFEARRPKEPAILAEISGIVSFG
KETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEA
PHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATI
VNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLAT
ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYH
QDRMRRRAAG
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4jk2 Chain I Residue 1502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jk2 Differential regulation by ppGpp versus pppGpp in Escherichia coli.
Resolution4.201 Å
Binding residue
(original residue number in PDB)		C888 C895 C898
Binding residue
(residue number reindexed from 1)		C871 C878 C881
Annotation score1
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4jk2, PDBe:4jk2, PDBj:4jk2
PDBsum4jk2
PubMed23620295
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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