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(-) Description

Title :  CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RESOLUTION. 2-METHYL-2,4-PENTANEDIOL AND MAGNESIUM BINDING.
 
Authors :  D. A. Adamiak, W. R. Rypniewski, J. Milecki, R. W. Adamiak
Date :  09 Mar 01  (Deposition) - 21 Sep 01  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  X-Ray, 2'-O-Merna Duplex, 2-Methyl-2, 4-Pentanediol, Magnesium, Groove Hydration And Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Adamiak, W. R. Rypniewski, J. Milecki, R. W. Adamiak
The 1. 19 A X-Ray Structure Of 2'-O-Me(Cgcgcg)(2) Duplex Shows Dehydrated Rna With 2-Methyl-2, 4-Pentanediol In The Minor Groove.
Nucleic Acids Res. V. 29 4144 2001
PubMed-ID: 11600703  |  Reference-DOI: 10.1093/NAR/29.20.4144
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))- 3'
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3OMC6Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
4OMG6Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREOMG A:2 , HOH A:224 , HOH A:225 , HOH A:226 , HOH A:228 , HOH A:229BINDING SITE FOR RESIDUE MG A 101
2AC2SOFTWAREOMG B:2 , HOH B:219 , HOH B:221 , HOH B:222 , HOH B:227 , HOH B:232BINDING SITE FOR RESIDUE MG B 102
3AC3SOFTWAREOMC A:5 , HOH A:219 , HOH A:221 , OMC B:5 , HOH B:217 , HOH B:223 , HOH B:224BINDING SITE FOR RESIDUE MG A 103
4AC4SOFTWAREHOH A:208 , HOH A:212 , HOH A:218 , HOH A:222BINDING SITE FOR RESIDUE MG A 104
5AC5SOFTWAREHOH B:206 , HOH B:207 , HOH B:226 , HOH B:231BINDING SITE FOR RESIDUE MG B 105
6AC6SOFTWAREOMG A:2 , OMC A:3 , OMG A:4 , OMG A:6 , HOH A:213BINDING SITE FOR RESIDUE MPD A 201
7AC7SOFTWAREOMC A:5 , OMG A:6 , OMG B:2 , OMC B:3 , OMG B:6 , HOH B:216BINDING SITE FOR RESIDUE MPD B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I7J)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1I7J)

(-) 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:RNA  Length:6
                                    
                   1i7j A 1 cgcgcg 6
                            ||||||
                            ||||||
                            1-OMC|
                             2-OMG
                              3-OMC
                               4-OMG
                                5-OMC
                                 6-OMG


Chain B from PDB  Type:RNA  Length:6
                                    
                   1i7j B 1 cgcgcg 6
                            ||||||
                            ||||||
                            1-OMC|
                             2-OMG
                              3-OMC
                               4-OMG
                                5-OMC
                                 6-OMG
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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 1I7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1I7J)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

310d 310D CONTAINS THE SAME 2'-O-METHYLATED RNA, AT ROOM TEMPERATURE AND HIGHER HYDRATION STATE.