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PDBsum entry 310d
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ligands metals links
RNA PDB id
310d

 

 

 

 

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Contents
Ligands
OMC-OMG-OMC-OMG-
OMC-OMG ×2
Metals
_MG ×2
Waters ×44
PDB id:
310d
Name: RNA
Title: Crystal structure of 2'-o-me(cgcgcg)2: an RNA duplex at 1.3 a resolution. Hydration pattern of 2'-o-methylated RNA
Structure: RNA (5'-r( (Omc)p (Omg)p (Omc)p (Omg)p (Omc)p (Omg))-3'). Chain: a, b. Engineered: yes
Source: Synthetic construct. Organism_taxid: 32630
Biol. unit: Dimer (from PQS)
Resolution:
1.30Å     R-factor:   0.172    
Authors: D.A.Adamiak,J.Milecki,R.W.Adamiak,Z.Dauter,W.R.Rypniewski
Key ref: D.A.Adamiak et al. (1997). Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA. Nucleic Acids Res, 25, 4599-4607. PubMed id: 9358171
Date:
25-May-96     Release date:   24-Jun-97    
 Headers
 References

 

 
Nucleic Acids Res 25:4599-4607 (1997)
PubMed id: 9358171  
 
 
Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.
D.A.Adamiak, J.Milecki, M.Popenda, R.W.Adamiak, Z.Dauter, W.R.Rypniewski.
 
  ABSTRACT  
 
The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20087997 M.Egli, and P.S.Pallan (2010).
Crystallographic studies of chemically modified nucleic acids: a backward glance.
  Chem Biodivers, 7, 60-89.  
20358065 R.Zhang, and L.A.Eriksson (2010).
Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group.
  Phys Chem Chem Phys, 12, 3690-3697.  
19333476 P.S.Pallan, T.P.Prakash, F.Li, R.L.Eoff, M.Manoharan, and M.Egli (2009).
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.
  Chem Commun (Camb), (), 2017-2019.
PDB codes: 3ey1 3ey2 3ey3
17300110 E.Rozners, D.Katkevica, and R.Strömberg (2007).
Oligoribonucleotide analogues containing a mixed backbone of phosphodiester and formacetal internucleoside linkages, together with vicinal 2'-O-methyl groups.
  Chembiochem, 8, 537-545.  
17439958 J.H.Lee, and A.Pardi (2007).
Thermodynamics and kinetics for base-pair opening in the P1 duplex of the Tetrahymena group I ribozyme.
  Nucleic Acids Res, 35, 2965-2974.  
16953416 M.Hägerlöf, P.Papsai, C.S.Chow, and S.K.Elmroth (2006).
More pronounced salt dependence and higher reactivity for platination of the hairpin r(CGCGUUGUUCGCG) compared with d(CGCGTTGTTCGCG).
  J Biol Inorg Chem, 11, 974-990.  
14715922 E.Rozners, and J.Moulder (2004).
Hydration of short DNA, RNA and 2'-OMe oligonucleotides determined by osmotic stressing.
  Nucleic Acids Res, 32, 248-254.  
15292450 M.Popenda, J.Milecki, and R.W.Adamiak (2004).
High salt solution structure of a left-handed RNA double helix.
  Nucleic Acids Res, 32, 4044-4054.
PDB code: 1t4x
12056901 M.Kaul, and D.S.Pilch (2002).
Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16S rRNA.
  Biochemistry, 41, 7695-7706.  
11809888 T.C.Mou, and D.M.Gray (2002).
The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications.
  Nucleic Acids Res, 30, 749-758.  
11600703 D.A.Adamiak, W.R.Rypniewski, J.Milecki, and R.W.Adamiak (2001).
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, 29, 4144-4153.
PDB code: 1i7j
12404373 P.Auffinger, and E.Westhof (2001).
Hydrophobic Groups Stabilize the Hydration Shell of 2'-O-Methylated RNA Duplexes.
  Angew Chem Int Ed Engl, 40, 4648-4650.  
9692952 V.Tereshko, S.Portmann, E.C.Tay, P.Martin, F.Natt, K.H.Altmann, and M.Egli (1998).
Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues.
  Biochemistry, 37, 10626-10634.
PDB codes: 410d 411d 412d
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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