Structure of PDB 8syl Chain C Binding Site BS03

Receptor Information
>8syl Chain C (length=271) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITT
RHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGER
RYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKG
GQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHM
LRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQ
TKGKKTRSNKRTDKFIVRRRS
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 chain8syl Chain C Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8syl Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		T223 G234 N239
Binding residue
(residue number reindexed from 1)		T222 G233 N238
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0019843 rRNA binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0032297 negative regulation of DNA-templated DNA replication initiation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:1990082 DnaA-L2 complex
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8syl, PDBe:8syl, PDBj:8syl
PDBsum8syl
PubMed37537169
UniProtP60422|RL2_ECOLI Large ribosomal subunit protein uL2 (Gene Name=rplB)

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