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(-) Description

Title :  BASE-TETRAD SWAPPING RESULTS IN DIMERIZATION OF RNA QUADRUPLEXES: IMPLICATIONS FOR FORMATION OF I-MOTIF RNA OCTAPLEX
 
Authors :  B. Pan, K. Shi, M. Sundaralingam
Date :  31 Aug 05  (Deposition) - 07 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Rna, Tetraplex, Octaplex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pan, K. Shi, M. Sundaralingam
Base-Tetrad Swapping Results In Dimerization Of Rna Quadruplexes: Implications For Formation Of The I-Motif Rna Octaplex.
Proc. Natl. Acad. Sci. Usa V. 103 3130 2006
PubMed-ID: 16492787  |  Reference-DOI: 10.1073/PNAS.0507730103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*(BGM)P*GP*UP*GP*U)-3'
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1BGM8Mod. Nucleotide8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
2K11Ligand/IonPOTASSIUM ION
3SR1Ligand/IonSTRONTIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC4SOFTWAREG A:5 , U A:6 , K A:212 , G B:5 , U B:6 , G C:5 , U C:6 , G D:5 , U D:6BINDING SITE FOR RESIDUE K A 211
02AC5SOFTWAREG A:3 , G A:5 , K A:211 , K A:213 , G B:3 , G B:5 , G C:3 , G C:5 , G D:3 , G D:5BINDING SITE FOR RESIDUE K A 212
03AC9SOFTWAREBGM A:2 , G A:3 , K A:212 , K A:214 , BGM B:2 , G B:3 , BGM C:2 , G C:3 , BGM D:2 , G D:3BINDING SITE FOR RESIDUE K A 213
04AD1SOFTWAREBGM A:2 , K A:213 , HOH A:236 , BGM B:2 , BGM C:2 , BGM D:2 , U E:1 , U F:1 , U G:1 , U H:1BINDING SITE FOR RESIDUE K A 214
05AD2SOFTWAREU A:1 , HOH A:236 , U B:1 , U C:1 , U D:1 , BGM E:2 , K E:216 , BGM F:2 , BGM G:2 , BGM H:2BINDING SITE FOR RESIDUE K A 215
06AD3SOFTWAREG A:3 , U A:4 , U A:6 , HOH A:223 , HOH A:225 , HOH C:222 , HOH C:237BINDING SITE FOR RESIDUE SR A 219
07AD4SOFTWAREHOH B:56 , G C:3 , U C:4 , U C:6BINDING SITE FOR RESIDUE K C 220
08AD5SOFTWAREK A:215 , BGM E:2 , G E:3 , K E:217 , BGM F:2 , G F:3 , BGM G:2 , G G:3 , BGM H:2 , G H:3BINDING SITE FOR RESIDUE K E 216
09AD6SOFTWAREG E:3 , G E:5 , K E:216 , K E:218 , G F:3 , G F:5 , G G:3 , G G:5 , G H:3 , G H:5BINDING SITE FOR RESIDUE K E 217
10BC1SOFTWAREG E:5 , U E:6 , K E:217 , G F:5 , U F:6 , G G:5 , U G:6 , G H:5 , U H:6BINDING SITE FOR RESIDUE K E 218
11BC2SOFTWAREG F:3 , U F:4 , U F:6 , HOH F:228 , HOH F:233 , HOH H:18BINDING SITE FOR RESIDUE K F 221
12BC3SOFTWAREHOH F:225 , U G:6BINDING SITE FOR RESIDUE K G 222

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AWE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AWE)

 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/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe A 1 UgGUGU 6
                             |    
                             |    
                             2-BGM


Chain B from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe B 1 UgGUGU 6
                             |    
                             2-BGM


Chain C from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe C 1 UgGUGU 6
                             |    
                             2-BGM


Chain D from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe D 1 UgGUGU 6
                             |    
                             2-BGM


Chain E from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe E 1 UgGUGU 6
                             |    
                             2-BGM


Chain F from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe F 1 UgGUGU 6
                             |    
                             2-BGM


Chain G from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe G 1 UgGUGU 6
                             |    
                             2-BGM


Chain H from PDB  Type:DNA/RNA  Length:6
                                    
                   2awe H 1 UgGUGU 6
                             |    
                             2-BGM
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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