Structure of PDB 3hoy Chain B Binding Site BS01

Receptor Information
>3hoy Chain B (length=1105) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSA
RTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKP
CVEDGFVIQDRETALDFIGRKEKRIQYAKDILQKEFLPHITQLEGFESRK
AFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKL
TKDIFRYMQRTVELAINAKTITSGLKYALATGNWGAGVSQVLNRYTYSST
LSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL
MSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHR
NPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVE
DDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEES
ILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASII
PFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTT
RAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFF
RSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVS
GEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVR
TTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS
RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGF
EVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPV
EGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLM
TVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTD
RSRDF
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3hoy Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R504 D505 M792 R857 R942 R1122 R1129 M1133
Binding residue
(residue number reindexed from 1)		R413 D414 M686 R751 R823 R1003 R1010 M1014
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D731
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003729 mRNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3hoy, PDBe:3hoy, PDBj:3hoy
PDBsum3hoy
PubMed19560423
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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