Structure of PDB 3gtg Chain A Binding Site BS05

Receptor Information
>3gtg Chain A (length=1442) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVL
STEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISF
NESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVAT
YMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTV
ISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA
KYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHK
MSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELS
QLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYW
VPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKD
NGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKV
VNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL
TAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSK
GSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVEN
SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHY
DNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLL
NTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEA
NWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRG
KNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQ
FLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLK
EILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEI
YYDPDPRSTVIPEDEEIIQLHFSLLDEQQSPWLLRLELDRAAMNDKDLTM
GQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHM
LKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETD
GVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASD
GSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL
FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLV
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 chain3gtg Chain A Residue 1736 [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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PDB3gtg Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
Resolution3.78 Å
Binding residue
(original residue number in PDB)		D481 D483 D485
Binding residue
(residue number reindexed from 1)		D479 D481 D483
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485 H1085
Catalytic site (residue number reindexed from 1) D479 D481 D483 H1083
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
View graph for
Cellular Component
External links
PDB RCSB:3gtg, PDBe:3gtg, PDBj:3gtg
PDBsum3gtg
PubMed19478184
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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