Structure of PDB 5nwt Chain D Binding Site BS01

Receptor Information

>5nwt Chain D (length=1358) Species: 83333 (Escherichia coli K-12)

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFK
PERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRE
RMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGG
MTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQ
LREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLR
PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYS
GRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKM
VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLH
PLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPII
VPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKV
RITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKK
HEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDN
LQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKP
DGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRL
VDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLK
PGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTIQVKNKGSIKLSNVKSVVN
SSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVA
NWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERT
AGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSG
DTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKE
TKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPH
DILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVN
AGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATES
FISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQD
RMRRRAAG

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: 5nwt Chain D Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nwt TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 reveal new and conserved regulatory strategies.
• Resolution: 3.76 Å
• Binding residue (original residue number in PDB): C70 C72 C85
• Binding residue (residue number reindexed from 1): C70 C72 C85
• 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:5nwt, PDBe:5nwt, PDBj:5nwt
• PDBsum: 5nwt
• PubMed: 26293966
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)