Structure of PDB 5ot2 Chain A Binding Site BS03

Receptor Information
>5ot2 Chain A (length=1412) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGL
NDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVC
ECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVP
SEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKDEPELRVLSTEEILNIF
KHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDD
LTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQ
PQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLEL
DQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGD
RIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVK
VIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQI
VSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIP
TPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQ
IIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNG
FSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLR
ESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQM
SACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQ
EFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLG
NVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPS
LLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIR
RIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQ
RDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG
EMVGVLAAQSIGEPATQMTLNKKVTSGVPRLKEILNVAKNMKTPSLTVYL
EPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEII
QLHFQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDN
DEKLIIRCRVVREEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVP
SPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIE
AGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRS
NTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFD
VMIDEESLVKYM
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ot2 Mechanism of RNA polymerase II stalling by DNA alkylation.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		I250 S251 F252 D483 D485
Binding residue
(residue number reindexed from 1)		I239 S240 F241 D472 D474
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D470 D472 D474
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: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: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
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
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:5ot2, PDBe:5ot2, PDBj:5ot2
PDBsum5ot2
PubMed29087308
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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