Structure of PDB 8w8o Chain D Binding Site BS05

Receptor Information
>8w8o Chain D (length=1481) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILVPVEKRQLLT
DEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVAL
YRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAE
EEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPL
AEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVV
VPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFE
DDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDA
RMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLD
SGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRL
KKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLT
DILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFK
PFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNR
APTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSF
AQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGL
EFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVA
HGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDV
PQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDA
VIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVT
QAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFE
VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHE
IVVREADCGTTNYISVPLFQPDVTRSLRLRKRADIEAGLYGRVLAREVEV
LGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCY
GYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTQGLPRVIELFEARRPKAK
AVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEA
GQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIV
VRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLL
MGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRL
IPAGTGSDFVRFTQVVDQKTLKAIEEARKEA
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 chain8w8o Chain D Residue 1602 [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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PDB8w8o Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
Resolution2.512 Å
Binding residue
(original residue number in PDB)		C58 C73 C76
Binding residue
(residue number reindexed from 1)		C56 C71 C74
Annotation score1
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8w8o, PDBe:8w8o, PDBj:8w8o
PDBsum8w8o
PubMed38990947
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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