Structural investigations of calcium-binding molecules. 4. Calcium binding to aminocarboxylates. Crystal structures of Ca(CaEDTA).7H2O and Na(CaNTA)

Barnett, B.L.; Uchtman, Vernon A.

doi:10.1021/ic50200a007

Cited by 90 publications

(51 citation statements)

References 8 publications

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“…Bond lengths and bond angles for the structure are given in Table 3. This structure is very similar to the crystal structure of NaCaNTA (Barnett & Uchtman, 1979). Although the two structures are not isomorphous (as shown by powder diffraction analyses), both utilize the crystallographic symmetry of the cubic space group P213 in a similar manner.…”

Section: C-c'-o-msupporting

confidence: 60%

“…The stability constants of many NTA complexes have been determined and tabulated (Sillen & Martell, 1964). The crystal structures of the triprotic acid (Stanford, 1967), the monohydrated trisodium salt (Daly, 1967) and a variety of metal-NTA complexes (Barnett & Uchtman, 1979;Battaglia, Corradi & Tani, 1975;Butcher & Penfold, 1976;Fomenko, Kopaneva, Porai-Koshits & Polynova, 1974;Fomenko, Polynova & Porai-Koshits, 1975a, b;Hoard, Silverton & Silver-0108-7681/84/040377-05501.50 ton, 1968;Martin & Jacobsen, 1972;Whitlow, 1972Whitlow, , 1973Wieghardt, Quiltzsch, Weiss & Nuber, 1980) have been reported. The versatility of the NTA ion as a sequestering agent prompted our investigation of the title compounds.…”

Section: Introductionmentioning

confidence: 99%

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Structures of sodium zinc nitrilotriacetate monohydrate (173 K) and disodium hydrogen nitrilotriacetate (293 K)

Oliver¹,

Barnett²,

Strickland³

1984

Acta Crystallogr Sect B

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NaZn(C6H6NO6).H20: Mr =295"44, orthorhombic, P212121, a = 7.869 (4), b =9.783 (6), c = 12.292 (6) A,, V = 946-3 A, 3, Z = 4, Dx = 2.07 gcm -3, A (So Kc~) = 0.71073A,, /z=27.4cm -I Final R=0.052 for 859 unique reflections. The nitrilotriacetate ion is coordinated to the Zn 2+ ion in a tetradentate fashion. The remaining two octahedral sites about the Zn 2÷ ion are occupied by O atoms of different nitrilotriacetate ions. A comparison of the structure with other published structures identifies a common geometry, termed the 'butterfly' geometry, for transition-metal complexes with nitrilotriacetate ligands. The Na ÷ ions bridge the nitrilotriacetatozinc ions thereby holding the structure intact. The water molecule is coordinated to the five-coordinate Na ÷ ion.

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Section: C-c'-o-msupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Structures of sodium zinc nitrilotriacetate monohydrate (173 K) and disodium hydrogen nitrilotriacetate (293 K)

Oliver¹,

Barnett²,

Strickland³

1984

Acta Crystallogr Sect B

Self Cite

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“…However, coordination about Ca2+ is considerably more fluxional, Ca2+-binding sites of six, seven, and eight ligands having been observed (36)(37)(38). Given that there are a multiplicity of different site sizes and coordination environments in a large RNA molecule (39)(40)(41) Nondenaturing polyacrylamide gel electrophoresis provides a rapid, convenient means for exploring the substrate binding event independently and directly.…”

Section: Discussionmentioning

confidence: 99%

Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena.

Pyle

McSwiggen

Cech

1990

Proc. Natl. Acad. Sci. U.S.A.

143

167

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Like protein enzymes, RNA enzymes (ribozymes) provide specific binding sites for their substrates. We now show that equilibrium dissociation constants for complexes between the Tetrahymena ribozyme and its RNA substrates and products can be directly measured by electrophoresis in polyacrylamide gels containing divalent cations. Binding is 103-to 104-fold tighter (4-5 kcal/mol at 42C) than expected from base-pairing interactions alone, implying that tertiary interactions also contribute to energetic stabilization. Binding decreases with single base changes in the substrate, substitution of deoxyribose sugars, and lower Mg2+ concentration. Ca2+, which enables the ribozyme to fold but is unable to mediate efficient RNA cleavage, promotes weaker substrate binding than Mg2+. This indicates that Mg2& has special roles in both substrate binding and catalysis. Mutagenesis of a region near the internal guide sequence disrupts substrate binding, whereas binding is not significantly affected by a mutation of the guanosine-binding site. This approach should be generally useful for analysis of ribozyme variants independent of their catalytic activities.Ribozymes derived from the self-splicing intervening sequence (IVS) of Tetrahymena rRNA catalyze phosphodiester bond cleavage of oligonucleotide substrates (1, 2). The mechanism for this reaction is similar to the first step in selfsplicing of the pre-rRNA (3). Substrate recognition is mediated by base-pairing interactions between an internal guide sequence (IGS) within the ribozyme and a complementary substrate (4-6). A schematic of this interaction is shown in Fig. 1. Given this model, one should be able to estimate the interaction energy by using rules developed for prediction of duplex stability (7)(8)(9). For a circular form of the same IVS, however, kinetic results suggest that oligonucleotides may bind to the active site with a greater affinity than expected for simple duplex formation (10, 11).Nondenaturing gel electrophoresis has been extensively used for studying nucleic acid-protein associations (12)(13)(14)(15)(16)(17). Complexes between RNA moieties have also been observed in native gels (18)(19)(20). Here we show that ribozyme-substrate complexes are stable in nondenaturing polyacrylamide gels containing Mg2' or Ca2+. The ability to partition free and ribozyme-bound RNA substrate makes it possible to quantitatively study factors contributing to the energetics of association. METHODSRNA Preparation. The L-21 Sca I ribozyme used in this study is a shortened form of the Tetrahymena thermophila pre-rRNA IVS, lacking the first 21 and last 5 nucleotides (the 3' end being determined by a Sca I site in the DNA template). This ribozyme is 388 nucleotides in length, and G414 has been deleted in order to study reactions in the presence of exogenous guanosine. The preparation of this ribozyme and its oligonucleotide substrates has been described (2). Oligonucleotide products were transcribed from the same DNA templates as the substrates, but ATP was omitted to cause ...

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“…This procedure involves estimating the relative proportions of graphic data are available for such a complex or for a calcium serine phosphate. X-ray data are, however, available for crystalline serine phosphate [17], calcium acetate [18], calcium EDTA and calcium NTA complexes [19], and these data were therefore used to construct a model of this component. On this basis the calcium appears to be bound to both the carboxylate and the phosphate ester groups.…”

Section: Research Articlesmentioning

confidence: 99%

Structural studies of a phosphatidyl serine-amorphous calcium phosphate complex

Taylor

Simkiss

Simmons

et al. 1998

CMLS, Cell. Mol. Life Sci.

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A phosphatidyl serine-amorphous calcium phosphate complex has been synthesized as a model of the matrix vesicle system that is associated with the induction of mineral deposition in bone, cartilage and dentine. The complex has been studied using a novel technique of subtractive extended X-ray absorption fine structure (EXAFS). This enables spectra of the components of the molecules to be subtracted from the complex so as to identify the sites of interaction. The results suggest there is a movement in the nitrogen atom of the phosphatidyl serine which approaches the calcium atom in the mineral phase. This interpretation would link the membrane structure of the vesicle to the structure of the mineral in a way that could explain some of its roles in biomineralization.

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Structural investigations of calcium-binding molecules. 4. Calcium binding to aminocarboxylates. Crystal structures of Ca(CaEDTA).7H2O and Na(CaNTA)

Cited by 90 publications

References 8 publications

Structures of sodium zinc nitrilotriacetate monohydrate (173 K) and disodium hydrogen nitrilotriacetate (293 K)

Structures of sodium zinc nitrilotriacetate monohydrate (173 K) and disodium hydrogen nitrilotriacetate (293 K)

Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena.

Structural studies of a phosphatidyl serine-amorphous calcium phosphate complex

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