Structure of PDB 3i4n Chain B

Receptor sequence
>3i4nB (length=1125) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYE
KVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLI
AQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREG
SSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEM
LKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPH
ITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLL
AQLFKTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKK
AMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGL
VCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVP
HQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIRE
KELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYT
WSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHAT
TFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYN
VRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQE
DSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMK
HGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIV
DQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDM
PFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTD
ITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMV
DDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKE
RLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA
AKLLFQELMAMNITPRLYTDRSRDF
3D structure
PDB3i4n Molecular basis of transcriptional mutagenesis at 8-oxoguanine
ChainB
Resolution3.9 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) D751
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 dna B D505 R942 R1122 R1129 D434 R843 R1023 R1030
BS02 dna B D505 K507 D434 K436
BS03 rna B A477 Q481 R766 Y769 Q776 K987 R1020 R1124 A406 Q410 R680 Y683 Q690 K888 R921 R1025
BS04 ZN B C1163 C1185 C1064 C1086
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:3i4n, PDBe:3i4n, PDBj:3i4n
PDBsum3i4n
PubMed19758983
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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