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(-) Description

Title :  TWO DIVALENT METAL IONS AND CONFORMATIONAL CHANGES PLAY ROLES IN THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION- G12A MUTANT IN ZN2+
 
Authors :  A. Mir, J. Chen, D. Neau, B. L. Golden
Date :  29 Aug 15  (Deposition) - 07 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribozyme, Hammerhead, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Mir, J. Chen, K. Robinson, E. Lendy, J. Goodman, D. Neau, B. L. Golden
Two Divalent Metal Ions And Conformational Changes Play Roles In The Hammerhead Ribozyme Cleavage Reaction.
Biochemistry V. 54 6369 2015
PubMed-ID: 26398724  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00824

(-) Compounds

Molecule 1 - RNA (48-MER)
    ChainsA
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsTHIS RNA WAS MADE BY IN VITRO TRANSCRIPTION
    SyntheticYES
 
Molecule 2 - 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)- R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'
    ChainsB
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsSYNTHESIZED OLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1ZN13Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:29binding site for residue ZN A 101
02AC2SOFTWAREG A:18binding site for residue ZN A 102
03AC3SOFTWAREG A:30binding site for residue ZN A 103
04AC4SOFTWAREG A:1binding site for residue ZN A 104
05AC5SOFTWAREG A:2binding site for residue ZN A 105
06AC6SOFTWAREG A:11binding site for residue ZN A 107
07AC7SOFTWAREG A:23binding site for residue ZN A 108
08AC8SOFTWAREG B:10binding site for residue ZN B 101
09AC9SOFTWAREA B:13 , ZN B:105binding site for residue ZN B 102
10AD1SOFTWAREG B:2binding site for residue ZN B 103
11AD2SOFTWAREC B:12 , A B:13 , G B:14 , ZN B:102binding site for residue ZN B 105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DH8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DH8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DH8)

(-) Exons   (0, 0)

(no "Exon" information available for 5DH8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:RNA  Length:48
                                                                               
                  5dh8 A  1 GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACAAAACGCCCA 48
                                    10        20        30        40        

Chain B from PDB  Type:DNA/RNA  Length:20
                                                   
                  5dh8 B  1 GGGCGUCUGGGCAGUACCCA 20
                                    10        20

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DH8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DH8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DH8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DH8)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

5dh6 5dh7 5di2 5di4