Structure of PDB 5w51 Chain B Binding Site BS04

Receptor Information
>5w51 Chain B (length=1089) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATLP
YIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVI
QDRETALDFIGRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGY
MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFR
YMQRTLAINAKTITSGLKYALATGNWGEQKKARAGVSQVLNRYTYSSTLS
HLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT
DPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET
LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHK
ELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIAMQPE
DLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRN
TYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL
PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYG
MSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP
ISKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFA
SRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLL
SKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKL
MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFG
EMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFE
CKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
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 chain5w51 Chain B Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5w51 Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
Resolution3.404 Å
Binding residue
(original residue number in PDB)		C1163 C1185
Binding residue
(residue number reindexed from 1)		C1032 C1054
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D720
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:5w51, PDBe:5w51, PDBj:5w51
PDBsum5w51
PubMed28933854
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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