Structure of PDB 3fki Chain B Binding Site BS01

Receptor Information
>3fki Chain B (length=1125) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSA
RTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKP
CVEDGFVIQDRETALDFIGREKRIQYAKDILQKEFLPHITQLEGFESRKA
FFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLT
KDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSS
RAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPA
ETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSP
DATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELK
IFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEYTWSS
LLNEGLVEYIDAEEEESILIAMQPEDLEPAEANDLDVDPAKRIRVSHHAT
TFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYN
VRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQE
DSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMK
HGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIV
DQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDM
PFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTD
ITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMV
DDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKE
RLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA
AKLLFQELMAMNITPRLYTDRSRDF
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 chain3fki Chain B Residue 1225 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3fki Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data
Resolution3.88 Å
Binding residue
(original residue number in PDB)		C1163 C1166 C1185
Binding residue
(residue number reindexed from 1)		C1064 C1067 C1086
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D751
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3fki, PDBe:3fki, PDBj:3fki
PDBsum3fki
PubMed19289466
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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