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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2'- DEOXYGUANOSINE RIBOSWITCH BOUND TO GUANOSINE
 
Authors :  O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Date :  23 Jun 11  (Deposition) - 17 Aug 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Three-Way Junction, Riboswitch, 2'-Deoxy Guanosine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Structural Principles Of Nucleoside Selectivity In A 2'-Deoxyguanosine Riboswitch.
Nat. Chem. Biol. V. 7 748 2011
PubMed-ID: 21841796  |  Reference-DOI: 10.1038/NCHEMBIO.631

(-) Compounds

Molecule 1 - RNA (68-MER)
    ChainsA, B
    EngineeredYES
    Other DetailsDG RIBOSWITCH
    Other Details - SourceIN VITRO TRANSCRIBED RNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1CCC2Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2GMP2Ligand/IonGUANOSINE
3GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4MG3Ligand/IonMAGNESIUM ION
5SIN1Ligand/IonSUCCINIC ACID
6SO48Ligand/IonSULFATE ION
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2GMP1Ligand/IonGUANOSINE
3GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
5SIN1Ligand/IonSUCCINIC ACID
6SO45Ligand/IonSULFATE ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2GMP1Ligand/IonGUANOSINE
3GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4MG-1Ligand/IonMAGNESIUM ION
5SIN-1Ligand/IonSUCCINIC ACID
6SO43Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA A:30 , C A:31 , C A:55 , C A:57 , C A:58 , G A:59 , C A:80 , U A:81BINDING SITE FOR RESIDUE GMP A 120
02AC2SOFTWAREC A:58 , G A:59BINDING SITE FOR RESIDUE MG A 228
03AC3SOFTWAREC A:24 , C A:25 , G A:86BINDING SITE FOR RESIDUE SO4 A 211
04AC4SOFTWAREC A:64 , A A:65BINDING SITE FOR RESIDUE SO4 A 212
05AC5SOFTWAREA A:30 , A A:79 , C A:80 , U A:81BINDING SITE FOR RESIDUE SO4 A 213
06AC6SOFTWAREC A:39 , A A:40 , U A:41 , HOH A:91BINDING SITE FOR RESIDUE SO4 A 216
07AC7SOFTWAREC A:68 , HOH A:180BINDING SITE FOR RESIDUE SO4 A 229
08AC8SOFTWAREC A:57 , C A:58BINDING SITE FOR RESIDUE SIN A 301
09AC9SOFTWAREA B:30 , C B:31 , A B:54 , C B:55 , C B:57 , C B:58 , G B:59 , C B:80 , U B:81BINDING SITE FOR RESIDUE GMP B 120
10BC1SOFTWAREA B:32 , C B:61 , A B:77 , G B:78BINDING SITE FOR RESIDUE MG B 172
11BC2SOFTWAREC B:24 , C B:25BINDING SITE FOR RESIDUE SO4 B 214
12BC3SOFTWAREC B:64 , A B:65BINDING SITE FOR RESIDUE SO4 B 217
13BC4SOFTWAREC B:39 , A B:40 , U B:41BINDING SITE FOR RESIDUE SO4 B 219

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SKZ)

(-) 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)

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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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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:68
                                                                                                   
                  3skz A 22 gGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUc 89
                            |       31        41        51        61        71        81       |
                            |                                                                 89-CCC
                           22-GTP                                                               

Chain B from PDB  Type:RNA  Length:68
                                                                                                   
                  3skz B 22 gGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUc 89
                            |       31        41        51        61        71        81       |
                            |                                                                 89-CCC
                           22-GTP                                                               

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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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 Related Entries

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(-) Related Entries Specified in the PDB File

3ski 3skl 3skr 3skt 3skw