Structure of PDB 7o4j Chain A Binding Site BS03

Receptor Information
>7o4j Chain A (length=1430) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRADEPELRVLSTE
EILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNES
QRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMD
NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISG
DPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYV
IRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSM
MAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLC
AVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPD
WDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGM
LIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNF
WLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAK
HGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSF
INIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYL
RGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNT
TRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTD
HTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWP
LPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNE
IIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLR
SVVHPGEMVGVLAAQSIGEPATQMKVTSGVPRLKEILNVAKNMKTPSLTV
YLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEE
IIQLHFSLLSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDL
FVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLR
GVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDP
TRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDV
MTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGV
SENVILGQMAPIGTGAFDVMIDEESLVKYM
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain7o4j Chain A Residue 1803 [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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PDB7o4j Structure of RNA polymerase II pre-initiation complex at 2.9 angstrom defines initial DNA opening.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D481 D483 D485
Binding residue
(residue number reindexed from 1)		D476 D478 D480
Annotation score1
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7o4j, PDBe:7o4j, PDBj:7o4j
PDBsum7o4j
PubMed34133942
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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