PDBsum entry 1i7j

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ligands metals links
MPD ×2
_MG ×5
Waters ×65
PDB id:
Name: RNA
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.
Structure: 5'-r( (Omc)p (Omg)p (Omc)p (Omg)p (Omc)p (Omg))- 3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
1.19Å     R-factor:   0.155    
Authors: D.A.Adamiak,W.R.Rypniewski,J.Milecki,R.W.Adamiak
Key ref: D.A.Adamiak et al. (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. PubMed id: 11600703 DOI: 10.1093/nar/29.20.4144
09-Mar-01     Release date:   21-Sep-01    


DOI no: 10.1093/nar/29.20.4144 Nucleic Acids Res 29:4144-4153 (2001)
PubMed id: 11600703  
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.
D.A.Adamiak, W.R.Rypniewski, J.Milecki, R.W.Adamiak.
The crystal and molecular structure of 2'-O-Me(CGCGCG)(2) has been determined at 1.19 A resolution, at 100 K, using synchrotron radiation. The structure in space group P3(2)12 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O(6) and N(7) of guanosine and N(4) of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)(2) structure in the P3(2)12 and P6(1)22 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18252773 E.Kierzek, R.Kierzek, W.N.Moss, S.M.Christensen, T.H.Eickbush, and D.H.Turner (2008).
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
  Nucleic Acids Res, 36, 1770-1782.  
18658118 W.Rypniewski, D.A.Adamiak, J.Milecki, and R.W.Adamiak (2008).
Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.
  RNA, 14, 1845-1851.
PDB codes: 3czw 3d0m
17461975 D.Plewczynski, M.Hoffmann, M.von Grotthuss, K.Ginalski, and L.Rychewski (2007).
In silico prediction of SARS protease inhibitors by virtual high throughput screening.
  Chem Biol Drug Des, 69, 269-279.  
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.  
17895397 H.Li, R.Liang, D.H.Turner, L.J.Rothberg, and S.Duan (2007).
Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure.
  RNA, 13, 2034-2041.  
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.  
16682562 A.L.Jackson, J.Burchard, D.Leake, A.Reynolds, J.Schelter, J.Guo, J.M.Johnson, L.Lim, J.Karpilow, K.Nichols, W.Marshall, A.Khvorova, and P.S.Linsley (2006).
Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing.
  RNA, 12, 1197-1205.  
16699193 W.Rypniewski, M.Vallazza, M.Perbandt, S.Klussmann, L.J.Delucas, C.Betzel, and V.A.Erdmann (2006).
The first crystal structure of an RNA racemate.
  Acta Crystallogr D Biol Crystallogr, 62, 659-664.
PDB codes: 2g32 2gpm 2gq4 2gq5 2gq6 2gq7
16155181 E.Kierzek, A.Ciesielska, K.Pasternak, D.H.Mathews, D.H.Turner, and R.Kierzek (2005).
The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.
  Nucleic Acids Res, 33, 5082-5093.  
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
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