Structure of PDB 8w8n Chain D

Receptor sequence

>8w8nD (length=1484) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILVPVEKRQLLT
DEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVAL
YRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAE
EEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPL
AEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVV
VPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFE
DDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDA
RMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLD
SGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRL
KKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLT
DILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFK
PFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNR
APTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSF
AQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGL
EFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVA
HGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDV
PQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDA
VIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVT
QAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFE
VPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHE
IVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVE
VLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKC
YGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTITQGLPRVIELFEARRP
KAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDY
VEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHI
EIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWK
PLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVIL
GRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

3D structure

• PDB: 8w8n Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.
• Chain: D
• Resolution: 2.693 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	D	R586 K610 R622 R628 A705 T1088 A1089 Y1093 Q1441	R582 K606 R618 R624 A701 T1084 A1085 Y1089 Q1423
BS02	dna	D	R1266 K1426	R1248 K1408
BS03	rna	D	R704 P706 N737 D739 D741 D743	R700 P702 N733 D735 D737 D739
BS04	ZN	D	C1112 C1194 C1201 C1204	C1108 C1190 C1197 C1200
BS05	ZN	D	C58 C73	C56 C71
BS06	MG	D	D739 D741 D743	D735 D737 D739
BS07	MG	D	W897 I900	W893 I896

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:8w8n, PDBe:8w8n, PDBj:8w8n
• PDBsum: 8w8n
• PubMed: 38990947
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)