Structure of PDB 8red Chain D Binding Site BS04

Receptor Information
>8red Chain D (length=1330) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPER
DGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMG
HIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTN
LERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLRE
ELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV
PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAV
DALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRS
VITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVER
EEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV
CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPS
QDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRIT
EYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISK
MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEI
ISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT
ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGS
IIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV
AQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGT
ADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDL
ARGHIINKGEAIGVIAAQSIGEPGTQLTMAAESSIQVKNKGSIKLSNVKS
VVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGE
TVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQSSLVVLDSAERRPALK
IVDAQGNDVAQYFLPGKAIVQLEDGVQISSGDTLARIPQGGLPRVADLFE
ARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQL
NVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGV
KINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANG
KVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRG
LKENVIVGRLIPAGTGYAYHQDRMRRRAAG
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain8red Chain D Residue 1501 [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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PDB8red Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		D460 D462 D464
Binding residue
(residue number reindexed from 1)		D457 D459 D461
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8red, PDBe:8red, PDBj:8red
PDBsum8red
PubMed38170755
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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