Structure of PDB 8w8p Chain D Binding Site BS02

Receptor Information

>8w8p Chain D (length=1497) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFR
AEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQ
PLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMN
VVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLA
VAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGID
DAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVT
HEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLARE
VEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVADITQG
LPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKL
PKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKV
YRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNE
RLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGK
KDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

Ligand information

>8w8p Chain H (length=24)

tataatgggagctgtcacggatgc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8w8p Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
• Resolution: 3.165 Å
• Binding residue (original residue number in PDB): R1266 K1426
• Binding residue (residue number reindexed from 1): R1261 K1421

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

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:8w8p, PDBe:8w8p, PDBj:8w8p
• PDBsum: 8w8p
• PubMed: 38990947
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)