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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VS RIBOZYME - G638A MUTANT
 
Authors :  J. A. Piccirilli, N. B. Suslov, S. Dasgupta, H. Huang, D. M. J. Lilley, P.
Date :  19 Aug 14  (Deposition) - 30 Sep 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.07
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Na, Dimer, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. B. Suslov, S. Dasgupta, H. Huang, J. R. Fuller, D. M. Lilley, P. A. Rice, J. A. Piccirilli
Crystal Structure Of The Varkud Satellite Ribozyme.
Nat. Chem. Biol. V. 11 840 2015
PubMed-ID: 26414446  |  Reference-DOI: 10.1038/NCHEMBIO.1929

(-) Compounds

Molecule 1 - VS RIBOZYME RNA
    Chains: A
    Engineered: YES
    Mutation: YES
    Organism Scientific: NEUROSPORA
    Organism Taxid: 5140
    Other Details: IN VITRO TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1GDP1Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
2K5Ligand/IonPOTASSIUM ION
3MG9Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GDP2Mod. NucleotideGUANOSINE-5'-DIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:906 , HOH A:907BINDING SITE FOR RESIDUE MG A 801
02AC2SOFTWAREHOH A:911 , HOH A:912 , HOH A:913 , HOH A:914 , HOH A:915 , HOH A:916BINDING SITE FOR RESIDUE MG A 803
03AC3SOFTWAREU A:669BINDING SITE FOR RESIDUE K A 804
04AC4SOFTWAREC A:758 , HOH A:917 , HOH A:918 , HOH A:919 , HOH A:920 , HOH A:921 , HOH A:922BINDING SITE FOR RESIDUE MG A 805
05AC5SOFTWAREHOH A:923 , HOH A:924 , HOH A:925 , HOH A:926 , HOH A:927 , HOH A:928BINDING SITE FOR RESIDUE MG A 806
06AC6SOFTWAREHOH A:929 , HOH A:930 , HOH A:931 , HOH A:932 , HOH A:933 , HOH A:934BINDING SITE FOR RESIDUE MG A 807
07AC7SOFTWAREHOH A:909 , HOH A:910BINDING SITE FOR RESIDUE MG A 808
08AC8SOFTWAREG A:704 , U A:705 , HOH A:901BINDING SITE FOR RESIDUE K A 809
09AC9SOFTWAREG A:740 , C A:741BINDING SITE FOR RESIDUE K A 810
10BC1SOFTWAREC A:764BINDING SITE FOR RESIDUE K A 811
11BC2SOFTWAREC A:674BINDING SITE FOR RESIDUE MG A 813

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R4V)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

(no "Exon" information available for 4R4V)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:RNA  Length:186
                                                                                                                                                                                                                          
                 4r4v A 600 gGCGCUGUGUCGCAAUCUGCGAAGGGCGUCGUCGGCCCAAGCGGUAGUAAGCAGGGAACUCACCUCCAAUGAAACACAUUGUCGUAGCAGUUGACUACUGUUAUGUGAUUGGUAGAGGCUAAGUGACGGUAUUGGCGUAAGCCAAUACCGCAGCACAGCACAAGCCCGCUUGCGAGAUUACAGCGC 785
                            |      609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779      
                            |                                                                                                                                                                                         
                          600-GDP
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4R4V)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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4r4p