Structure of PDB 7dic Chain A Binding Site BS02

Receptor Information
>7dic Chain A (length=646) Species: 243273 (Mycoplasmoides genitalium G37) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKLQGILTLGNKNSGFIRSLDDDKTVYYVHYSNLTGALDGDLVEFCKLDK
PQFGDKFDAAVITILKRARILYAGNFLVDQNEFALEYKIVADNPRFYLTM
IVNPDSIPNNLASNTKIAFQIDEYDPDNNLCKVSVQQVLGNNDDPLINIK
AIMLDNSIVFETNDVVEQHANKLSFDTEEQHKAYRQDLTDLAFVTVDPTT
SKDLADAIYVKTIPTGFVLYVAIADVAHYVNRNSEIDIEAKHKTSSIYLP
GHYVVPMLPEQLSNQLCSLNPAQKRYVVVCEISFDNQGRIKTNKLYPATI
ISKNRFSYDQVNKWLNNKSELNCDETVINSLKAAFTLSDLIQAQRQKRGT
IDLSHKETEIVVDEHYFPIKINFLVHDKAETMIENLMVVANETVAWVLTN
NKIALPYRVHPRPSKKKLQSLIETVGELNITKPQFNLDTVTSSQIASWLN
ENKDNPSYEIFVILLLRTLGKAFYSVNPLMHFSIGSNHYTHFTSPIRRYI
DLTIHRLLWMHLFTPDQFTDNERDQLKQELEKIADTVNDTEIKIINCERN
ANDYLTTLLLSKQIGKTFSGFISAITSFGIFMRMDENNFDGLIKITTIPD
DFFIFEKEKMVLKGRKTNKVYKIGDRLEAKLSEIDFIQKRAILTLI
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 chain7dic Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7dic Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Resolution2.242 Å
Binding residue
(original residue number in PDB)		D276 D285
Binding residue
(residue number reindexed from 1)		D197 D206
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D276 D282 A284 D285 Y387 R576
Catalytic site (residue number reindexed from 1) D197 D203 A205 D206 Y308 R497
Enzyme Commision number 3.1.13.1: exoribonuclease II.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0008859 exoribonuclease II activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0016070 RNA metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7dic, PDBe:7dic, PDBj:7dic
PDBsum7dic
PubMed33788943
UniProtP47350|RNR_MYCGE Ribonuclease R (Gene Name=rnr)

[Back to BioLiP]