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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A24U/U25A/A46G/C74U MUTANT XPT-PBUX GUANINE RIBOSWITCH APTAMER DOMAIN IN COMPLEX WITH 2,6-DIAMINOPURINE
 
Authors :  C. D. Stoddard, J. J. Trausch, J. Widmann, J. Marcano, R. Knight, R. T. Ba
Date :  30 May 12  (Deposition) - 27 Feb 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  B
Keywords :  Three-Way Junction With Distal Tertiary Interaction, Genetic Regulatory Element, 2, 6-Diaminopurine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Stoddard, J. Widmann, J. J. Trausch, J. G. Marcano-Velazquez, R. Knight, R. T. Batey
Nucleotides Adjacent To The Ligand-Binding Pocket Are Linke To Activity Tuning In The Purine Riboswitch.
J. Mol. Biol. V. 425 1596 2013
PubMed-ID: 23485418  |  Reference-DOI: 10.1016/J.JMB.2013.02.023

(-) Compounds

Molecule 1 - A24U/U25A/A46G/C74U MUTANT OF THE B. SUBTILIS XPT-PBUX GUANINE RIBOSWITCH APTAMER DOMAIN
    ChainsB
    EngineeredYES
    Other DetailsT7 RNAP TRANSCRIPT
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
16AP1Ligand/Ion9H-PURINE-2,6-DIAMINE
2NCO9Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA B:21 , U B:22 , U B:47 , U B:51 , A B:52 , A B:73 , U B:74 , U B:75 , HOH B:667BINDING SITE FOR RESIDUE 6AP B 101
02AC2SOFTWAREG B:29 , U B:30 , A B:66 , U B:67 , HOH B:655 , HOH B:677 , HOH B:688 , HOH B:850 , HOH B:856 , HOH B:982 , HOH B:1030 , HOH B:1031BINDING SITE FOR RESIDUE NCO B 102
03AC3SOFTWAREG B:38 , G B:56 , G B:57 , C B:58 , HOH B:658 , HOH B:756 , HOH B:848 , HOH B:927 , HOH B:998 , HOH B:1025BINDING SITE FOR RESIDUE NCO B 103
04AC4SOFTWAREC B:39 , G B:55 , G B:56 , G B:57 , G B:68 , U B:69 , HOH B:697 , HOH B:763 , HOH B:1135BINDING SITE FOR RESIDUE NCO B 104
05AC5SOFTWAREU B:30 , G B:31 , G B:32 , A B:65 , A B:66 , HOH B:607 , HOH B:638 , HOH B:641 , HOH B:727BINDING SITE FOR RESIDUE NCO B 105
06AC6SOFTWAREG B:37 , G B:38 , HOH B:629 , HOH B:715 , HOH B:953 , HOH B:1132 , HOH B:1148BINDING SITE FOR RESIDUE NCO B 106
07AC7SOFTWAREC B:41 , G B:42 , C B:53 , C B:54 , HOH B:614 , HOH B:674 , HOH B:858 , HOH B:881 , HOH B:1023BINDING SITE FOR RESIDUE NCO B 107
08AC8SOFTWAREA B:45 , G B:46 , U B:47 , HOH B:676 , HOH B:721 , HOH B:754 , HOH B:894 , HOH B:1004 , HOH B:1059 , HOH B:1157BINDING SITE FOR RESIDUE NCO B 108
09AC9SOFTWAREA B:21 , U B:22 , HOH B:1130BINDING SITE FOR RESIDUE NCO B 109
10BC1SOFTWAREU B:36 , G B:42 , C B:43 , G B:72 , A B:73 , HOH B:875BINDING SITE FOR RESIDUE NCO B 110

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FEP)

(-) Exons   (0, 0)

(no "Exon" information available for 4FEP)

(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain B from PDB  Type:RNA  Length:67
                                                                                                  
                  4fep B 15 GGACAUAUAUACGCGUGGAUAUGGCACGCGAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCC 81
                                    24        34        44        54        64        74       

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1u8d 4fe5 4fej 4fel 4fen 4feo