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(-) Description

Title :  STRUCTURAL RATIONALIZATION OF A LARGE DIFFERENCE IN RNA AFFINITY DESPITE A SMALL DIFFERENCE IN CHEMISTRY BETWEEN TWO 2'-O-MODIFIED NUCLEIC ACID ANALOGS
 
Authors :  R. Pattanayek, L. Sethaphong, C. Pan, M. Prhavc, T. P. Prakash, M. Manoharan, M. Egli
Date :  26 Oct 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rna Mimetic Methylamino Amide Analog, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pattanayek, L. Sethaphong, C. Pan, M. Prhavc, T. P. Prakash, M. Manoharan, M. Egli
Structural Rationalization Of A Large Difference In Rna Affinity Despite A Small Difference In Chemistry Between Two 2'-O-Modified Nucleic Acid Analogues.
J. Am. Chem. Soc. V. 126 15006 2004
PubMed-ID: 15547979  |  Reference-DOI: 10.1021/JA044637K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
    Chains: A, B, C, D
    Engineered: YES
    Other Details: SYNTHETICALLY CREATED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NMS4Mod. Nucleotide1-(O2-(2-METHYLAMINO-2-OXO-ETHYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NMS2Mod. Nucleotide1-(O2-(2-METHYLAMINO-2-OXO-ETHYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NMS2Mod. Nucleotide1-(O2-(2-METHYLAMINO-2-OXO-ETHYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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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:DNA  Length:10
                                          
                 1xux A   1 GCGTAtACGC  10
                                 |  10
                                 6-NMS


Chain B from PDB  Type:DNA  Length:10
                                          
                 1xux B 101 GCGTAtACGC 110
                                 | 110
                               106-NMS


Chain C from PDB  Type:DNA  Length:10
                                          
                 1xux C 201 GCGTAtACGC 210
                                 | 210
                               206-NMS


Chain D from PDB  Type:DNA  Length:10
                                          
                 1xux D 301 GCGTAtACGC 310
                                 | 310
                               306-NMS
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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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  1xux
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