Polymeric metal–nucleotide complexes. The crystal structures of [(C9H12N3O8P)Cd(H2O).H2O]
 n
 and [(C9H12N3O8P)Co(H2O)]
 n
 formed between cadmium(II) or cobalt(II) ions and cytidine 5'-monophosphate

Clark, G.R.; Orbell, John D.

doi:10.1107/s0567740878006755

Cited by 35 publications

(6 citation statements)

References 16 publications

(20 reference statements)

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“…Therefore, three representative examples referring to M 2+ complexes formed with CMP 2or dCMP 2are shown in Fig. 4 [17,51,52]. In all instances, in agreement with the discussions in the preceding section, the (d)CMP 2-ligands are present in the solid state in their more stable anti conformation.…”

Section: Discussionsupporting

confidence: 84%

“…Exactly this binding mode is observed in the solid state ( Fig. 4A) where Co 2+ , with a distorted tetrahedral coordination sphere, forms a strong bond to N3 (1.987 Å ) and no further interaction with the nucleobase occurs [51,53]. For Ni(Cyd) 2+ also a sole N3-Ni 2+ interaction must be surmised, based on the stability data ( Fig.…”

Section: Discussionmentioning

confidence: 84%

“…Oxygen atoms are represented by black balls and hydrogen atoms are omitted for clarity, though in C two hydrogen bonds are indicated. A In the polymeric Co(CMP) [51] the tetrahedral metal ion is bound to N3 of the cytosine residue (bond length for N3-Co 2+ : 1.99 Å ) as well as to two oxygens of phosphate groups and to one water molecule. B In the polymeric Cd(dCMP) [52], binding of the octahedral Cd 2+ occurs to both N3 (2.30 Å ) and (C2)O (2.64 Å ); the other four sites are occupied by two oxygens of phosphate groups and two water molecules.…”

Section: Discussionmentioning

confidence: 99%

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A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

Knobloch

Sigel

2004

J Biol Inorg Chem

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The recently defined log K (M)(M)(L) versus pK(H)(H)(L) straight-line plots for L = pyridine-type (PyN) and ortho-aminopyridine-type (oPyN) ligands now allow the evaluation in a quantitative manner of the stability of the 1:1 complexes formed between cytidine (Cyd) and Ca(2+), Mg(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) (M(2+)); the corresponding stability constants, K(M)(M)(Cyd) including the acidity constant, K(H)(H)(Cyd) for the deprotonation of the (N3)H(+) site had been determined previously under exactly the same conditions as the mentioned plots. Since the stabilities of the M(PyN)(2+) and M(oPyN)(2+) complexes of Ca(2+) and Mg(2+) are practically identical, it is concluded that complex formation occurs in an outer-sphere manner, and this is in accord with the fact that in the p K(a) range 3-7 metal ion binding is independent of K(H)(H)(Pyn) or K(H)(H)(oPyN). Ca(Cyd)(2+) and Mg(Cyd)(2+) are more stable than the corresponding (outer-sphere) M(PyN)(2+) complexes and this means that the C2 carbonyl group of Cyd must participate, next to N3 which is most likely outer-sphere, in metal ion binding, leading thus to chelates; these have formation degrees of about 50% and 35%, respectively. Co(Cyd)(2+) and Ni(Cyd)(2+) show no increased stability based on the log K(M)(M)(oPyN) versus pK(H)(H)(oPyN) hence, the (C2)O group does not participate in metal ion binding, but the inner-sphere coordination to N3 is strongly inhibited by the (C4)NH(2) group. In the M(Cyd)(2+) complexes of Mn(2+), Cu(2+), Zn(2+) and Cd(2+), this inhibiting effect on M(2+) binding at N3 is partially compensated by participation of the (C2)O group in complex formation and the corresponding chelates have formation degrees between about 30% (Zn(2+)) and 83% (Cu(2+)). The different structures of the mentioned chelates are discussed in relation to available crystal structure analyses. (1). There is evidence (crystal structure studies: Cu(2+), Zn(2+), Cd(2+)) that four-membered rings form, i.e. there is a strong M(2+) bond to N3 and a weak one to (C2)O. (2). By hydrogen bond formation to (C2)O of a metal ion-bound water molecule, six-membered rings, so-called semichelates, may form. (3). For Ca(2+) and Mg(2+), and possibly Mn(2+), and their Cyd complexes, six-membered chelates are also likely with (C2)O being inner-sphere (crystal structure) and N3 outer-sphere. (4). Finally, for these metal ions also complexes with a sole outer-sphere interaction may occur. All these types of chelates are expected to be in equilibrium with each other in solution, but, depending on the metal ion, either the one or the other form will dominate. Clearly, the cytidine residue is an ambivalent binding site which adjusts well to the requirements of the metal ion to be bound and this observation is of relevance for single-stranded nucleic acids and their interactions with metal ions. In addition, the anti- syn energy barrier has been estimated as being in the order of 6-7.5 kJ/mol for cytidine derivatives in aqueous solution at 25 degrees C.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

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A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

Knobloch

Sigel

2004

J Biol Inorg Chem

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“…(iv) In the polymeric Co(CMP) complex the metal ion coordinates to N3 (1.99 Å) and does not interact with (C2)O [86]; this agrees with the properties of Co(Cyd) 2+ for which equilibrium (13) is far to its left. However, considering the small slope of the Co(oPyN) 2+ reference line seen in Figure 6 (compare with the Mg 2+ situation) [59], it could well be that a significant amount of the metal ion in Co(Cyd) 2+ is also outersphere bound to N3.…”

Section: Cadmium(ii) Complexes Of Pyrimidine Derivativessupporting

confidence: 65%

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Sigel

Skilandat

Sigel

et al. 2012

Metal Ions in Life Sciences

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Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromaticnitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono-to the di-and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono-or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

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“…Co 2+ binds in a monodentate fashion to N3 (e.g. [25]) and the same was surmised for Ni 2+ , including the (U À H) À systems [10]. For the present study this means that Cu 2+ and Cd 2+ most likely form 4-membered rings involving (N3) À and (C2)S ( Fig.…”

Section: Some Considerations On the Structure Of The Complexes Formedmentioning

confidence: 81%

Extent of metal ion–sulfur binding in complexes of thiouracil nucleosides and nucleotides in aqueous solution

Odani

Kozłowski

Świa̧tek-Kozłowska

et al. 2007

Journal of Inorganic Biochemistry

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Polymeric metal–nucleotide complexes. The crystal structures of [(C₉H₁₂N₃O₈P)Cd(H₂O).H₂O]_n and [(C₉H₁₂N₃O₈P)Co(H₂O)]_n formed between cadmium(II) or cobalt(II) ions and cytidine 5'-monophosphate

Cited by 35 publications

References 16 publications

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Extent of metal ion–sulfur binding in complexes of thiouracil nucleosides and nucleotides in aqueous solution

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Polymeric metal–nucleotide complexes. The crystal structures of [(C9H12N3O8P)Cd(H2O).H2O] n and [(C9H12N3O8P)Co(H2O)] n formed between cadmium(II) or cobalt(II) ions and cytidine 5'-monophosphate

Cited by 35 publications

References 16 publications

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Extent of metal ion–sulfur binding in complexes of thiouracil nucleosides and nucleotides in aqueous solution

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Polymeric metal–nucleotide complexes. The crystal structures of [(C₉H₁₂N₃O₈P)Cd(H₂O).H₂O]_n and [(C₉H₁₂N₃O₈P)Co(H₂O)]_n formed between cadmium(II) or cobalt(II) ions and cytidine 5'-monophosphate