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(-) Description

Title :  STRUCTURAL VARIATIONS AND SOLVENT STRUCTURE OF UGGGGU QUADRUPLEXES STABILIZED BY SR2+ IONS
 
Authors :  A. C. Fyfe, P. W. Dunten, W. G. Scott
Date :  24 Oct 14  (Deposition) - 19 Nov 14  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.01
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (2x)
Biol. Unit 2:  E,F,G,H  (2x)
Keywords :  Rna Quadruplexes, Parallel-Stranded, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. Fyfe, P. W. Dunten, M. M. Martick, W. G. Scott
Structural Variations And Solvent Structure Of R(Uggggu) Quadruplexes Stabilized By Sr(2+) Ions.
J. Mol. Biol. V. 427 2205 2015
PubMed-ID: 25861762  |  Reference-DOI: 10.1016/J.JMB.2015.03.022

(-) Compounds

Molecule 1 - RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsRNA UGGGGU QUADRUPLEXES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (2x)ABCD    
Biological Unit 2 (2x)    EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2NA4Ligand/IonSODIUM ION
3SR7Ligand/IonSTRONTIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SR-1Ligand/IonSTRONTIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3SR-1Ligand/IonSTRONTIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:102 , G A:103 , G B:202 , G B:203 , G C:302 , G C:303 , G D:402 , G D:403BINDING SITE FOR RESIDUE SR A 901
02AC2SOFTWAREG A:104 , G A:105 , G B:204 , G B:205 , NA B:302 , G C:304 , G C:305 , G D:404 , G D:405BINDING SITE FOR RESIDUE SR B 301
03AC3SOFTWAREG A:105 , U A:106 , G B:205 , U B:206 , SR B:301 , NA B:303 , G C:305 , U C:306 , G D:405 , U D:406BINDING SITE FOR RESIDUE NA B 302
04AC4SOFTWAREU A:106 , HOH A:1019 , U B:206 , NA B:302 , U C:306BINDING SITE FOR RESIDUE NA B 303
05AC5SOFTWAREHOH A:1011 , HOH A:1028 , HOH A:1030 , U B:206 , HOH B:407 , HOH B:410 , HOH B:412BINDING SITE FOR RESIDUE CA B 304
06AC6SOFTWAREHOH B:435 , U C:306 , HOH C:503 , HOH C:508 , HOH C:518BINDING SITE FOR RESIDUE CA C 401
07AC7SOFTWAREHOH A:1004 , HOH B:425 , HOH B:432 , U C:301 , HOH C:501 , HOH C:515BINDING SITE FOR RESIDUE CA C 402
08AC8SOFTWAREG A:102 , G D:402 , G E:502 , G E:503 , HOH E:702 , HOH E:712 , HOH E:720BINDING SITE FOR RESIDUE CA D 9001
09AC9SOFTWAREHOH B:434 , HOH C:517 , U D:406 , HOH D:9506 , HOH D:9515BINDING SITE FOR RESIDUE CA D 9002
10BC1SOFTWAREG E:504 , G E:505 , G F:604 , G F:605 , NA F:701BINDING SITE FOR RESIDUE SR E 601
11BC2SOFTWAREG E:502 , G E:503 , G F:602 , G F:603BINDING SITE FOR RESIDUE SR E 602
12BC3SOFTWAREU B:201 , U E:501 , HOH E:707 , HOH E:711 , HOH E:716 , HOH E:718 , HOH G:904 , HOH G:907BINDING SITE FOR RESIDUE SR E 603
13BC4SOFTWAREHOH C:507 , U E:506 , HOH E:717 , HOH E:722 , HOH E:724 , HOH E:733BINDING SITE FOR RESIDUE CA E 604
14BC5SOFTWAREG E:505 , U E:506 , SR E:601 , G F:605 , U F:606BINDING SITE FOR RESIDUE NA F 701
15BC6SOFTWAREU F:606 , HOH F:802 , HOH F:810 , HOH F:815BINDING SITE FOR RESIDUE CA F 702
16BC7SOFTWAREG G:702 , G G:703 , G H:802 , G H:803BINDING SITE FOR RESIDUE SR G 801
17BC8SOFTWAREG G:704 , G G:705 , G H:804 , G H:805 , NA H:901BINDING SITE FOR RESIDUE SR G 802
18BC9SOFTWAREG A:103 , HOH D:9532 , G G:702 , G G:703 , HOH G:905 , HOH G:906 , HOH G:915BINDING SITE FOR RESIDUE CA G 803
19CC1SOFTWAREG G:705 , U G:706 , SR G:802 , G H:805 , U H:806BINDING SITE FOR RESIDUE NA H 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RNE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RNE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RNE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RNE)

(-) Exons   (0, 0)

(no "Exon" information available for 4RNE)

(-) Sequences/Alignments

Asymmetric 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:RNA  Length:6
                                      
                 4rne A 101 UGGGGU 106

Chain B from PDB  Type:RNA  Length:6
                                      
                 4rne B 201 UGGGGU 206

Chain C from PDB  Type:RNA  Length:6
                                      
                 4rne C 301 UGGGGU 306

Chain D from PDB  Type:RNA  Length:6
                                      
                 4rne D 401 UGGGGU 406

Chain E from PDB  Type:RNA  Length:6
                                      
                 4rne E 501 UGGGGU 506

Chain F from PDB  Type:RNA  Length:6
                                      
                 4rne F 601 UGGGGU 606

Chain G from PDB  Type:RNA  Length:6
                                      
                 4rne G 701 UGGGGU 706

Chain H from PDB  Type:RNA  Length:6
                                      
                 4rne H 801 UGGGGU 806

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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)

(no "SCOP Domain" information available for 4RNE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RNE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RNE)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4RNE)

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1j8g 4rkv