PDBsum entry 1i0f

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dna_rna metals links
Waters ×113
PDB id:
Name: DNA
Title: 1.6 a structure of the a-decamer gcgtatacgc with a single 2'-o-aminooxyethyl thymine in place of t6, ba-form
Structure: 5'-d( Gp Cp Gp Tp Ap (127)P Ap Cp Gp C)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
1.60Å     R-factor:   0.190     R-free:   0.212
Authors: V.Tereshko,C.J.Wilds,G.Minasov,T.P.Prakash,M.A.Maier, A.Howard,Z.Wawrzak,M.Manoharan,M.Egli
Key ref: V.Tereshko et al. (2001). Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res, 29, 1208-1215. PubMed id: 11222771 DOI: 10.1093/nar/29.5.1208
29-Jan-01     Release date:   04-Apr-01    


DOI no: 10.1093/nar/29.5.1208 Nucleic Acids Res 29:1208-1215 (2001)
PubMed id: 11222771  
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli.
The observation of light metal ions in nucleic acids crystals is generally a fortuitous event. Sodium ions in particular are notoriously difficult to detect because their X-ray scattering contributions are virtually identical to those of water and Na(+.)O distances are only slightly shorter than strong hydrogen bonds between well-ordered water molecules. We demonstrate here that replacement of Na(+) by K(+), Rb(+) or Cs(+) and precise measurements of anomalous differences in intensities provide a particularly sensitive method for detecting alkali metal ion-binding sites in nucleic acid crystals. Not only can alkali metal ions be readily located in such structures, but the presence of Rb(+) or Cs(+) also allows structure determination by the single wavelength anomalous diffraction technique. Besides allowing identification of high occupancy binding sites, the combination of high resolution and anomalous diffraction data established here can also pinpoint binding sites that feature only partial occupancy. Conversely, high resolution of the data alone does not necessarily allow differentiation between water and partially ordered metal ions, as demonstrated with the crystal structure of a DNA duplex determined to a resolution of 0.6 A.

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.  
20517991 M.Egli (2010).
Diffraction techniques in structural biology.
  Curr Protoc Nucleic Acid Chem, (), Unit 7.13.  
20198501 S.M.Perepelytsya, and S.N.Volkov (2010).
Intensities of DNA ion-phosphate modes in the low-frequency Raman spectra.
  Eur Phys J E Soft Matter, 31, 201-205.  
19690373 M.J.Schnieders, T.D.Fenn, V.S.Pande, and A.T.Brunger (2009).
Polarizable atomic multipole X-ray refinement: application to peptide crystals.
  Acta Crystallogr D Biol Crystallogr, 65, 952-965.  
  19255472 R.M.Leal, S.C.Teixeira, M.P.Blakeley, E.P.Mitchell, and V.T.Forsyth (2009).
A preliminary neutron crystallographic study of an A-DNA crystal.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 232-235.  
17242509 A.Volkov, M.Messerschmidt, and P.Coppens (2007).
Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures.
  Acta Crystallogr D Biol Crystallogr, 63, 160-170.  
17173143 M.Egli, P.Lubini, and P.S.Pallan (2007).
The long and winding road to the structure of homo-DNA.
  Chem Soc Rev, 36, 31-45.  
17288535 M.Egli, and P.S.Pallan (2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
  Annu Rev Biophys Biomol Struct, 36, 281-305.  
17406625 P.S.Pallan, and M.Egli (2007).
Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures.
  Nat Protoc, 2, 640-646.  
17378582 S.Khrapunov, and M.Brenowitz (2007).
Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein.
  Biochemistry, 46, 4876-4887.  
18060594 S.M.Perepelytsya, and S.N.Volkov (2007).
Counterion vibrations in the DNA low-frequency spectra.
  Eur Phys J E Soft Matter, 24, 261-269.  
17940138 Y.Timsit, and S.Bombard (2007).
The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.
  RNA, 13, 2098-2107.
PDB codes: 2r1s 2r20
16566588 F.Li, S.Sarkhel, C.J.Wilds, Z.Wawrzak, T.P.Prakash, M.Manoharan, and M.Egli (2006).
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
  Biochemistry, 45, 4141-4152.
PDB codes: 2fih 2fii 2fij 2fil
16170156 B.Diop-Frimpong, T.P.Prakash, K.G.Rajeev, M.Manoharan, and M.Egli (2005).
Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines.
  Nucleic Acids Res, 33, 5297-5307.
PDB code: 2axb
15869389 D.E.Draper, D.Grilley, and A.M.Soto (2005).
Ions and RNA folding.
  Annu Rev Biophys Biomol Struct, 34, 221-243.  
15739179 E.Stellwagen, Q.Dong, and N.C.Stellwagen (2005).
Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water.
  Biopolymers, 78, 62-68.  
16282586 J.Zhou, S.Krueger, and S.K.Gregurick (2005).
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution.
  Nucleic Acids Res, 33, 6361-6371.  
15858259 M.E.Than, S.Henrich, G.P.Bourenkov, H.D.Bartunik, R.Huber, and W.Bode (2005).
The endoproteinase furin contains two essential Ca2+ ions stabilizing its N-terminus and the unique S1 specificity pocket.
  Acta Crystallogr D Biol Crystallogr, 61, 505-512.  
16041074 T.Chatake, I.Tanaka, H.Umino, S.Arai, and N.Niimura (2005).
The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.
  Acta Crystallogr D Biol Crystallogr, 61, 1088-1098.
PDB codes: 1v9g 1woe
15501936 W.Ge, B.Schneider, and W.K.Olson (2005).
Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids.
  Biophys J, 88, 1166-1190.  
15951514 Y.Tsunaka, N.Kajimura, S.Tate, and K.Morikawa (2005).
Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle.
  Nucleic Acids Res, 33, 3424-3434.
PDB code: 2cv5
14960719 C.Cáceres, G.Wright, C.Gouyette, G.Parkinson, and J.A.Subirana (2004).
A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions.
  Nucleic Acids Res, 32, 1097-1102.
PDB codes: 1s45 1s47
15298889 M.Rueda, E.Cubero, C.A.Laughton, and M.Orozco (2004).
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?
  Biophys J, 87, 800-811.  
15465909 S.Y.Ponomarev, K.M.Thayer, and D.L.Beveridge (2004).
Ion motions in molecular dynamics simulations on DNA.
  Proc Natl Acad Sci U S A, 101, 14771-14775.  
12736317 E.Ennifar, P.Walter, and P.Dumas (2003).
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes.
  Nucleic Acids Res, 31, 2671-2682.
PDB codes: 1nlc 1nle 1o3z 1wvd 1y6s 1y6t 1y73 1y90 1y95 2oij
14500824 G.E.Sims, and S.H.Kim (2003).
Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes.
  Nucleic Acids Res, 31, 5607-5616.  
12598364 J.A.Subirana, and M.Soler-Lopez (2003).
Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.
  Annu Rev Biophys Biomol Struct, 32, 27-45.  
12786045 R.Das, T.T.Mills, L.W.Kwok, G.S.Maskel, I.S.Millett, S.Doniach, K.D.Finkelstein, D.Herschlag, and L.Pollack (2003).
Counterion distribution around DNA probed by solution X-ray scattering.
  Phys Rev Lett, 90, 188103.  
12717724 S.B.Howerton, A.Nagpal, and L.D.Williams (2003).
Surprising roles of electrostatic interactions in DNA-ligand complexes.
  Biopolymers, 69, 87-99.
PDB code: 1p20
12618190 V.Tereshko, E.Skripkin, and D.J.Patel (2003).
Encapsulating streptomycin within a small 40-mer RNA.
  Chem Biol, 10, 175-187.
PDB codes: 1nta 1ntb
12832804 X.Dong (2003).
X-ray crystallographic study of the possible binding sites of the monovalent cations in the Z-DNA structure.
  Acta Crystallogr D Biol Crystallogr, 59, 1336-1338.  
12169666 C.A.Davey, and T.J.Richmond (2002).
DNA-dependent divalent cation binding in the nucleosome core particle.
  Proc Natl Acad Sci U S A, 99, 11169-11174.  
12445769 J.Choe, S.Suresh, G.Wisedchaisri, K.J.Kennedy, M.H.Gelb, and W.G.Hol (2002).
Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
  Chem Biol, 9, 1189-1197.
PDB codes: 1jdj 1m66 1m67 1n1g
11904368 M.Egli, G.Minasov, L.Su, and A.Rich (2002).
Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution.
  Proc Natl Acad Sci U S A, 99, 4302-4307.
PDB codes: 1l2x 1l3d
12115142 B.Wellenzohn, W.Flader, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2001).
Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2.
  Biopolymers, 61, 276-286.  
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.