Structure of PDB 8s55 Chain B Binding Site BS03

Receptor Information
>8s55 Chain B (length=1130) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPI
DLQPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVD
ITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNEC
PLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLEN
SSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALG
FVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAK
PGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAAL
GRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGK
DFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFAS
TLSHLRRLNSPIGLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAY
ISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPE
QLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQ
KLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDD
LQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQ
AMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVA
IASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEK
PTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPTKRDCST
FLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGT
CGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKG
EIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIG
PTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQ
IAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKT
QISLVRMPYACKLLFQELMSMSIAPRMMSV
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8s55 Chain B Residue 1201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8s55 Three-step mechanism of promoter escape by RNA polymerase II
Resolution3.4 Å
Binding residue
(original residue number in PDB)		C1119 C1122 C1140
Binding residue
(residue number reindexed from 1)		C1075 C1078 C1096
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:0003682 chromatin binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8s55, PDBe:8s55, PDBj:8s55
PDBsum8s55
PubMed38604172
UniProtI3LGP4

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