Structure of PDB 2waq Chain A

Receptor sequence

>2waqA (length=841) Species: 2286 (Saccharolobus shibatae)

KNIKGIKFGILSPDEIRKMSVTAIITPGSVMDPRLGVIEPGQKCPTCGNT
LGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKY
SRIYNAIKKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKILTPSDIRE
RLEKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMAEDDLTHK
LVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEIPGLPPSK
HRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVG
VPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDL
RYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVL
KGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIIT
PRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVADVKIDLGEPA
ILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYVVI
KNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRF
VELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIP
GRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVL
NITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRT
GLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTV
RSLYGEVIQVAYGDDGVFPMYSAHGKTVDVNRIFERVVGWK

3D structure

• PDB: 2waq Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.
• Chain: A
• Resolution: 3.35 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	ZN	A	C58 C68 H71	C44 C54 H57
BS02	ZN	A	C98 V145	C84 V131
BS03	MG	A	D456 D458 D460	D418 D420 D422

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• 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
• GO:0005737 cytoplasm

External links

• PDB: RCSB:2waq, PDBe:2waq, PDBj:2waq
• PDBsum: 2waq
• PubMed: 19419240
• UniProt: B8YB53|RPO1N_SACSH DNA-directed RNA polymerase subunit Rpo1N (Gene Name=rpo1N)