Structure of PDB 6upy Chain B Binding Site BS04

Receptor Information
>6upy Chain B (length=1109) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKR
TKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVL
IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE
GSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLE
MLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFE
SRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLF
KKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNWGEQKKAMSSRAG
VSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNG
VWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVY
RPLFIVEDDGHKELKVRKGHIAKLMATEYQDVEEYTWSSLLNEGLVEYID
AEEEESILIAMQPEDLEPLDVDPAKRIRVSHHATTFTHCEIHPSMILGVA
ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKP
LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFR
SLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPG
VRVSGEDVIIGKTTPISAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLK
FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLII
NPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREH
GYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ
VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI
CGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNI
TPRLYTDRS
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 chain6upy Chain B Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6upy RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		C1163 C1166 C1182 C1185
Binding residue
(residue number reindexed from 1)		C1051 C1054 C1070 C1073
Annotation score1
Enzymatic activity
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:6upy, PDBe:6upy, PDBj:6upy
PDBsum6upy
PubMed32284409
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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