Structure of PDB 2ja6 Chain B

Receptor sequence
>2ja6B (length=1115) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDS
TLIISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSA
RTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKP
CVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQ
LEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQL
FKTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMS
SRAGVSQVLNRYTYSSTLSHLRRTNTPIKPRQLHNTHWGLVCPAETPEGQ
ACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVF
VNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAG
RVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLV
EYIDAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPS
MILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANIL
YYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSI
DRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDD
GLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQD
GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPD
LIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLL
REHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARG
PMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFR
VHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMA
MNITPRLYTDRSRDF
3D structure
PDB2ja6 CPD damage recognition by transcribing RNA polymerase II.
ChainB
Resolution4.0 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D741
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 rna B A477 Q776 K987 R1096 H1097 R1124 A403 Q680 K878 R987 H988 R1015
BS02 dna B R942 R1122 S1123 R1129 R833 R1013 S1014 R1020
BS03 ZN B C1163 C1185 C1054 C1076
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:2ja6, PDBe:2ja6, PDBj:2ja6
PDBsum2ja6
PubMed17290000
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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