Structure of PDB 3rf9 Chain A Binding Site BS01

Receptor Information
>3rf9 Chain A (length=355) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVTTKDGKINLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDE
MTDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYI
PEDDRATLCVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIV
GAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVT
LSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLA
AVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLI
PWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDDVIDRTKRT
LRKRM
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain3rf9 Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rf9 Structural basis for methyl transfer by a radical SAM enzyme.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		C125 L127 C129 C132 G179
Binding residue
(residue number reindexed from 1)		C116 L118 C120 C123 G170
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E105 C118 C125 C129 C132
Catalytic site (residue number reindexed from 1) E96 C109 C116 C120 C123
Enzyme Commision number 2.1.1.192: 23S rRNA (adenine(2503)-C(2))-methyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0002935 tRNA (adenine(37)-C2)-methyltransferase activity
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0019843 rRNA binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0070040 rRNA (adenine(2503)-C2-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
GO:0032259 methylation
GO:0046677 response to antibiotic
GO:0070475 rRNA base methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3rf9, PDBe:3rf9, PDBj:3rf9
PDBsum3rf9
PubMed21527678
UniProtP36979|RLMN_ECOLI Dual-specificity RNA methyltransferase RlmN (Gene Name=rlmN)

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