Structure of PDB 6koo Chain D Binding Site BS06

Receptor Information
>6koo Chain D (length=1258) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKI
FGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPV
THIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTL
EAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGG
EREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEY
FTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAA
FQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRN
NRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKS
LSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALEL
FKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRA
PTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEA
QAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQP
ASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELF
GHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLA
ERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEE
RADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIIT
IVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFI
NTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVEL
ADGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAA
GITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGE
PGTQLTMTGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIV
PDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSAD
PHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTI
IDSGSTEFLPGSLIDRAEFEAENRRVVAAGRPVLMGITKASLATDSWLSA
ASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQ
PTEEARAA
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 chain6koo Chain D Residue 2003 [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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PDB6koo RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D535 D537 D539
Binding residue
(residue number reindexed from 1)		D534 D536 D538
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6koo, PDBe:6koo, PDBj:6koo
PDBsum6koo
PubMed32127479
UniProtP9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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