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(-) Description

Title :  SAM-I RIBOSWITCH BEARING THE H. MARISMORTUI KT-7 VARIANT C-2BU
 
Authors :  L. Huang, D. M. J. Lilley
Date :  07 Oct 15  (Deposition) - 25 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A
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
    Chains: A
    Fragment: SAM BINDING DOMAIN
    Organism Scientific: THERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid: 119072
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric/Biological Unit (6, 30)
No.NameCountTypeFull Name
1BA21Ligand/IonBARIUM ION
2GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
3K4Ligand/IonPOTASSIUM ION
4MG2Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION
6SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
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:89 , BA A:104 , HOH A:2016 , HOH A:2017BINDING SITE FOR RESIDUE SAM A 101
02AC2SOFTWAREG A:50 , HOH A:2097BINDING SITE FOR RESIDUE BA A 102
03AC3SOFTWAREU A:81 , G A:82 , HOH A:2159BINDING SITE FOR RESIDUE BA A 103
04AC4SOFTWAREG A:11 , SAM A:101 , BA A:116 , HOH A:2021 , HOH A:2025 , HOH A:2028 , HOH A:2180BINDING SITE FOR RESIDUE BA A 104
05AC5SOFTWAREA A:70 , G A:71 , G A:79 , U A:80 , HOH A:2124 , HOH A:2134BINDING SITE FOR RESIDUE BA A 105
06AC6SOFTWAREA A:85 , G A:86 , HOH A:2161 , HOH A:2162 , HOH A:2163 , HOH A:2168BINDING SITE FOR RESIDUE BA A 106
07AC7SOFTWAREG A:18 , HOH A:2036 , HOH A:2037 , HOH A:2039 , HOH A:2040BINDING SITE FOR RESIDUE BA A 107
08AC8SOFTWAREBA A:120 , BA A:121 , HOH A:2070 , HOH A:2072 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE BA A 108
09AC9SOFTWAREGTP A:1 , HOH A:2001BINDING SITE FOR RESIDUE BA A 109
10BC1SOFTWAREG A:42 , G A:43 , HOH A:2082 , HOH A:2083 , HOH A:2085 , HOH A:2086 , HOH A:2181BINDING SITE FOR RESIDUE BA A 110
11BC2SOFTWAREG A:94 , HOH A:2176 , HOH A:2178 , HOH A:2179BINDING SITE FOR RESIDUE BA A 111
12BC3SOFTWAREA A:46 , G A:55 , HOH A:2088 , HOH A:2089 , HOH A:2091 , HOH A:2104 , HOH A:2105 , HOH A:2108BINDING SITE FOR RESIDUE BA A 112
13BC4SOFTWAREG A:15 , G A:16BINDING SITE FOR RESIDUE BA A 113
14BC5SOFTWAREU A:64 , U A:67 , HOH A:2058BINDING SITE FOR RESIDUE BA A 114
15BC6SOFTWAREG A:27 , G A:28 , HOH A:2059 , HOH A:2060 , HOH A:2062 , HOH A:2066BINDING SITE FOR RESIDUE BA A 115
16BC7SOFTWAREG A:11 , U A:64 , BA A:104 , BA A:122 , HOH A:2021BINDING SITE FOR RESIDUE BA A 116
17BC8SOFTWAREG A:21 , U A:22 , A A:34 , HOH A:2047 , HOH A:2052BINDING SITE FOR RESIDUE BA A 117
18BC9SOFTWAREG A:50 , HOH A:2098 , HOH A:2099 , HOH A:2182BINDING SITE FOR RESIDUE BA A 118
19CC1SOFTWAREG A:74 , HOH A:2136 , HOH A:2137 , HOH A:2141 , HOH A:2142 , HOH A:2183BINDING SITE FOR RESIDUE BA A 119
20CC2SOFTWAREG A:32 , BA A:108 , HOH A:2071 , HOH A:2072 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE BA A 120
21CC3SOFTWAREG A:32 , BA A:108 , HOH A:2070 , HOH A:2072 , HOH A:2075BINDING SITE FOR RESIDUE BA A 121
22CC4SOFTWAREA A:10 , G A:11 , BA A:116 , HOH A:2024BINDING SITE FOR RESIDUE BA A 122
23CC5SOFTWAREU A:4 , U A:5 , U A:88 , G A:89 , A A:90 , HOH A:2012 , HOH A:2170BINDING SITE FOR RESIDUE K A 123
24CC6SOFTWAREG A:11 , A A:62 , HOH A:2024 , HOH A:2027 , HOH A:2030 , HOH A:2114BINDING SITE FOR RESIDUE K A 124
25CC7SOFTWAREHOH A:2005 , HOH A:2010 , HOH A:2012 , HOH A:2165BINDING SITE FOR RESIDUE K A 125
26CC8SOFTWAREA A:62 , HOH A:2027 , HOH A:2029 , HOH A:2113 , HOH A:2114BINDING SITE FOR RESIDUE MG A 127
27CC9SOFTWAREC A:72 , G A:73 , G A:74 , HOH A:2134 , HOH A:2135 , HOH A:2137BINDING SITE FOR RESIDUE MG A 128
28DC1SOFTWAREC A:69 , A A:83 , A A:84BINDING SITE FOR RESIDUE NA A 129

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FJC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:RNA  Length:94
                                                                                                                             
                  5fjc A  1 gGCUUAUCAAGAGAGGGGGAGUGACUGGCGCGAAGAACCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG 94
                            |       10        20        30        40        50        60        70        80        90    
                            |                                                                                             
                            1-GTP
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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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

5fj0 STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS SIMPLE DUPLEX IN P4222 SPACE GROUP
5fj1 STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP IN P212121 SPACE GROUP
5fj4 STRUCTURE OF THE STANDARD KINK TURN HMKT-7 AS STEM LOOP BOUND WITH U1A AND L7AE PROTEINS