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(-) Description

Title :  THE LEADZYME STRUCTURE BOUND TO MG(H20)6(II) AT 1.8 A RESOLUTION
 
Authors :  J. E. Wedekind, D. B. Mckay
Date :  31 Jan 03  (Deposition) - 19 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Ribozyme, Leadzyme, Lead-Dependent Cleavage, Rna, Mg(H20) 62+, Bulged Nucleotides, Hydrated Magnesium, Pseudohelical Packing, Sticky Ends, Alternate Conformation, Homopurine Base Pairs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Wedekind, D. B. Mckay
Crystal Structure Of The Leadzyme At 1. 8 A Resolution: Metal Ion Binding And The Implications For Catalytic Mechanism And Allo Site Ion Regulation.
Biochemistry V. 42 9554 2003
PubMed-ID: 12911297  |  Reference-DOI: 10.1021/BI0300783
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'
    Chains: A, C, E, G
    Engineered: YES
    Other Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK.
    Synthetic: YES
 
Molecule 2 - 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
    Chains: B, D, F, H
    Engineered: YES
    Other Details: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, REPORTED BY PAN & UHLENBECK.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MG10Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:419 , HOH A:420 , HOH A:421 , HOH B:420 , HOH B:421 , HOH B:422BINDING SITE FOR RESIDUE MG A 417
02AC2SOFTWAREHOH A:422 , HOH A:423 , HOH A:424 , HOH A:425 , HOH B:423 , HOH B:424BINDING SITE FOR RESIDUE MG A 418
03AC3SOFTWAREHOH A:426 , HOH A:427 , HOH B:425 , HOH B:426 , HOH B:427 , HOH B:428BINDING SITE FOR RESIDUE MG B 419
04AC4SOFTWAREHOH G:229 , HOH G:230 , HOH G:231 , HOH G:232 , HOH G:233 , HOH H:228BINDING SITE FOR RESIDUE MG G 420
05AC5SOFTWAREHOH G:210 , HOH G:211 , HOH G:212 , HOH G:213 , HOH G:214 , HOH H:209BINDING SITE FOR RESIDUE MG G 421
06AC6SOFTWAREHOH G:235 , HOH G:238 , HOH H:234 , HOH H:236 , HOH H:237 , HOH H:239BINDING SITE FOR RESIDUE MG H 422
07AC7SOFTWAREHOH E:431 , HOH E:432 , HOH E:443 , HOH F:68 , HOH F:82 , HOH F:99BINDING SITE FOR RESIDUE MG E 423
08AC8SOFTWAREHOH E:453 , HOH E:454 , HOH E:459 , HOH E:469 , HOH E:477 , HOH F:81BINDING SITE FOR RESIDUE MG E 424
09AC9SOFTWAREHOH C:184 , HOH C:307 , HOH C:363 , HOH C:391 , HOH C:392 , HOH D:364BINDING SITE FOR RESIDUE MG C 425
10BC1SOFTWAREHOH C:131 , HOH C:137 , HOH C:166 , HOH D:160 , HOH D:178 , HOH D:371BINDING SITE FOR RESIDUE MG C 426

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NUJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NUJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:13
                                            
                  1nuj A 18 CGGACCGAGCCAG 30
                                    27   


Chain B from PDB  Type:RNA  Length:11
                                          
                  1nuj B 39 GCUGGGAGUCC 49
                                    48 


Chain C from PDB  Type:RNA  Length:13
                                            
                  1nuj C 18 CGGACCGAGCCAG 30
                                    27   


Chain D from PDB  Type:RNA  Length:11
                                          
                  1nuj D 39 GCUGGGAGUCC 49
                                    48 


Chain E from PDB  Type:RNA  Length:13
                                            
                  1nuj E 18 CGGACCGAGCCAG 30
                                    27   


Chain F from PDB  Type:RNA  Length:11
                                          
                  1nuj F 39 GCUGGGAGUCC 49
                                    48 


Chain G from PDB  Type:RNA  Length:13
                                            
                  1nuj G 18 CGGACCGAGCCAG 30
                                    27   


Chain H from PDB  Type:RNA  Length:11
                                          
                  1nuj H 39 GCUGGGAGUCC 49
                                    48
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 Classification and Annotation

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(-) Related Entries Specified in the PDB File

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