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(-) Description

Title :  SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UC
 
Authors :  L. Huang, D. M. J. Lilley
Date :  15 Oct 15  (Deposition) - 25 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rna, Kink Turn, Rna Motif, Sam-I Riboswitch (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Huang, J. Wang, D. M. J. Lilley
A Critical Base Pair In K-Turns Determines The Conformational Class Adopted, And Correlates With Biological Function.
Nucleic Acids Res. V. 44 5390 2016
PubMed-ID: 27016741  |  Reference-DOI: 10.1093/NAR/GKW201

(-) Compounds

Molecule 1 - SAM-I RIBOSWITCH
    ChainsA
    FragmentSAM BINDING DOMAIN
    Organism ScientificTHERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid119072
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1BA12Ligand/IonBARIUM ION
2K2Ligand/IonPOTASSIUM ION
3NA2Ligand/IonSODIUM ION
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BA-1Ligand/IonBARIUM ION
2K-1Ligand/IonPOTASSIUM ION
3NA-1Ligand/IonSODIUM ION
4SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREU A:7 , C A:8 , G A:11 , A A:45 , A A:46 , C A:47 , U A:57 , G A:58 , C A:59 , U A:88 , G A:89BINDING SITE FOR RESIDUE SAM A1095
02AC2SOFTWAREG A:86BINDING SITE FOR RESIDUE BA A1096
03AC3SOFTWAREG A:32BINDING SITE FOR RESIDUE BA A1097
04AC4SOFTWAREG A:1BINDING SITE FOR RESIDUE BA A1098
05AC5SOFTWAREG A:1 , G A:94 , BA A:1102BINDING SITE FOR RESIDUE BA A1113
06AC6SOFTWAREU A:64 , U A:67BINDING SITE FOR RESIDUE BA A1099
07AC7SOFTWAREG A:50BINDING SITE FOR RESIDUE BA A1100
08AC8SOFTWAREG A:74BINDING SITE FOR RESIDUE BA A1101
09AC9SOFTWAREG A:1 , BA A:1113BINDING SITE FOR RESIDUE BA A1102
10BC1SOFTWAREG A:11 , U A:64BINDING SITE FOR RESIDUE BA A1103
11BC2SOFTWAREA A:45 , G A:55BINDING SITE FOR RESIDUE BA A1104
12BC3SOFTWAREA A:36BINDING SITE FOR RESIDUE BA A1128
13BC4SOFTWAREA A:62 , U A:64 , C A:65BINDING SITE FOR RESIDUE NA A1105
14BC5SOFTWAREU A:4 , U A:5 , U A:88 , G A:89BINDING SITE FOR RESIDUE K A1106
15BC6SOFTWAREA A:70 , G A:71 , G A:79 , U A:80BINDING SITE FOR RESIDUE K A1107
16BC7SOFTWAREU A:81 , G A:82BINDING SITE FOR RESIDUE NA A1108

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
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Chain A from PDB  Type:RNA  Length:94
                                                                                                                             
                  5fkf A  1 GGCUUAUCAAGAGAGGGCGAGCGACUGGCGCGAAGAUCCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG 94
                                    10        20        30        40        50        60        70        80        90    

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(-) CATH Domains  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5fk1 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UG
5fk2 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS GG
5fk3 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CC
5fk4 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UU
5fk5 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS AA
5fk6 SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CA
5fkd SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS UA
5fke SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS GU
5fkg SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CG
5fkh SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT 3BN IS CU