Structure of PDB 7rdq Chain D

Receptor sequence

>7rdqD (length=1366) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAI
DPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVL
ADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLE
ALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLP
PDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEK
RMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGK
RVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVK
AARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLV
EGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS
PASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEV
ALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGK
RLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLR
LGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKL
LQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLY
VMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYF
ISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVP
LFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDV
HLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV
GIVAAQSIGEPGTQLTTQGLPRVIELFEARRPKAKAVISEIDGVVRIEET
EEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLL
EAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGD
SRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLS
AASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQV
VDQKTLKAIEEARKEA

3D structure

• PDB: 7rdq Structural and mechanistic basis of reiterative transcription initiation.
• Chain: D
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

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 S596 K610 R615 R622 T1088 A1089 Q1441 N1442	R465 S475 K489 R494 R501 T967 A968 Q1305 N1306
BS02	ZN	D	C1112 C1194 C1204	C991 C1073 C1083
BS03	ZN	D	C58 C60 C76	C56 C58 C74
BS04	MG	D	D739 D741 D743	D618 D620 D622
BS05	MG	D	W897 E898 I900	W776 E777 I779

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:7rdq, PDBe:7rdq, PDBj:7rdq
• PDBsum: 7rdq
• PubMed: 35082149
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)