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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2'- DEOXYGUANOSINE RIBOSWITCH BOUND TO GUANOSINE-5'-MONOPHOSPHATE
 
Authors :  O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Date :  24 Jun 11  (Deposition) - 17 Aug 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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)
    Chains: A, B
    Engineered: YES
    Other Details: IN VITRO TRANSCRIBED RNA
    Synthetic: YES

 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  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2CCC2Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
3GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4SIN1Ligand/IonSUCCINIC ACID
5SO47Ligand/IonSULFATE ION
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
3GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4SIN1Ligand/IonSUCCINIC ACID
5SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
3GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
4SIN-1Ligand/IonSUCCINIC ACID
5SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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:81 , A A:82 , U A:83BINDING SITE FOR RESIDUE 5GP A 120
02AC2SOFTWAREA B:30 , C B:31 , C B:57 , C B:58 , G B:59 , C B:80 , U B:81 , A B:82 , U B:83BINDING SITE FOR RESIDUE 5GP B 120
03AC3SOFTWAREC A:25BINDING SITE FOR RESIDUE SO4 A 211
04AC4SOFTWAREC A:64 , A A:65BINDING SITE FOR RESIDUE SO4 A 212
05AC5SOFTWAREC B:24 , C B:25BINDING SITE FOR RESIDUE SO4 B 214
06AC6SOFTWAREC A:39 , A A:40BINDING SITE FOR RESIDUE SO4 A 216
07AC7SOFTWAREC B:64 , A B:65BINDING SITE FOR RESIDUE SO4 B 217
08AC8SOFTWAREC B:39 , A B:40 , U B:41BINDING SITE FOR RESIDUE SO4 B 219
09AC9SOFTWAREC A:68BINDING SITE FOR RESIDUE SO4 A 229
10BC1SOFTWAREC A:57 , C A:58BINDING SITE FOR RESIDUE SIN A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SLQ)

 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:68
                                                                                                   
                  3slq A 22 gGCCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGGUc 89
                            |       31        41        51        61        71        81       |
                            |                                                                 89-CCC
                           22-GTP                                                               


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

3ski 3skl 3skt 3skw 3skz 3slm