Structure of PDB 2bh2 Chain A Binding Site BS03

Receptor Information
>2bh2 Chain A (length=418) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARA
KVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKH
DVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPI
LAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSA
DREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFI
QVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGV
EGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDP
ARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAML
DMFPHTGHLESMVLFSRV
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 chain2bh2 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2bh2 A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function
Resolution2.15 Å
Binding residue
(original residue number in PDB)		C81 C87 C90 Q93 F148 C162 P163 I164
Binding residue
(residue number reindexed from 1)		C67 C73 C76 Q79 F134 C148 P149 I150
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.190: 23S rRNA (uracil(1939)-C(5))-methyltransferase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005506 iron ion binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0070041 rRNA (uridine-C5-)-methyltransferase activity
Biological Process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0009451 RNA modification
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0070475 rRNA base methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2bh2, PDBe:2bh2, PDBj:2bh2
PDBsum2bh2
PubMed15766524
UniProtP55135|RLMD_ECOLI 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD (Gene Name=rlmD)

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