Structure of PDB 2nvz Chain B Binding Site BS03

Receptor Information
>2nvz Chain B (length=1096) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKVFIGR
LPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSA
GNIVQVFKKAAPSPISHVAEIRSALEKGSISTLQVKLYGREGSSARTIKA
TLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDG
FVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGY
MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFR
YMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTY
SSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSC
ISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPA
RLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDE
SLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILI
AMQPEDLEPAEDVDPAKRIRVSATTFTHCEIHPSMILGVAASIIPFPDHN
QSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYL
KFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ
EKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVII
GKTTPISRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG
DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLI
ECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHT
GKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGG
LRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNH
NQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRD
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 chain2nvz Chain B Residue 1307 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2nvz Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
Resolution4.3 Å
Binding residue
(original residue number in PDB)		C1166 C1182 C1185
Binding residue
(residue number reindexed from 1)		C1039 C1055 C1058
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D725
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
View graph for
Cellular Component
External links
PDB RCSB:2nvz, PDBe:2nvz, PDBj:2nvz
PDBsum2nvz
PubMed17129781
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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