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PubMed2003

Dimethylsulfoxide as a ligand for RhI and IrI complexes--isolation, structure, and reactivity towards X-H bonds (X=H, OH, OCH3).

Novel neutral and cationic Rh(I) and Ir(I) complexes that contain only DMSO molecules as dative ligands with S-, O-, and bridging S,O-binding modes were isolated and characterized. The neutral derivatives [RhCl(DMSO)(3)] (1) and [IrCl(DMSO)(3)] (2) were synthesized from the dimeric precursors [M(2)Cl(2)(coe)(4)] (M=Rh, Ir; COE=cyclooctene). The dimeric Ir(I) compound [Ir(2)Cl(2)(DMSO)(4)] (3) was obtained from 2. The first example of a square-planar complex with a bidentate S,O-bridging DMSO ligand, [(coe)(DMSO)Rh(micro-Cl)(micro-DMSO)RhCl(DMSO)] (4), was obtained by treating [Rh(2)Cl(2)(coe)(4)] with three equivalents of DMSO. The mixed DMSO-olefin complex [IrCl(cod)(DMSO)] (5, COD=cyclooctadiene) was generated from [Ir(2)Cl(2)(cod)(2)]. Substitution reactions of these neutral systems afforded the complexes [RhCl(py)(DMSO)(2)] (6), [IrCl(py)(DMSO)(2)] (7), [IrCl(iPr(3)P)(DMSO)(2)] (8), [RhCl(dmbpy)(DMSO)] (9, dmbpy=4,4'-dimethyl-2,2'-bipyridine), and [IrCl(dmbpy)(DMSO)] (10). The cationic O-bound complex [Rh(cod)(DMSO)(2)]BF(4) (11) was synthesized from [Rh(cod)(2)]BF(4). Treatment of the cationic complexes [M(coe)(2)(O=CMe(2))(2)]PF(6) (M=Rh, Ir) with DMSO gave the mixed S- and O-bound DMSO complexes [M(DMSO)(2)(DMSO)(2)]PF(6) (Rh=12; Ir=in situ characterization). Substitution of the O-bound DMSO ligands with dmbpy or pyridine resulted in the isolation of [Rh(dmbpy)(DMSO)(2)]PF(6) (13) and [Ir(py)(2)(DMSO)(2)]PF(6) (14). Oxidative addition of hydrogen to [IrCl(DMSO)(3)] (2) gave the kinetic product fac-[Ir(H)(2)Cl(DMSO)(3)] (15) which was then easily converted to the more thermodynamically stable product mer-[Ir(H)(2)Cl(DMSO)(3)] (16). Oxidative addition of water to both neutral and cationic Ir(I) DMSO complexes gave the corresponding hydrido-hydroxo addition products syn-[(DMSO)(2)HIr(micro-OH)(2)(micro-Cl)IrH(DMSO)(2)][IrCl(2)(DMSO)(2)] (17) and anti-[(DMSO)(2)(DMSO)HIr(micro-OH)(2)IrH(DMSO)(2)(DMSO)][PF(6)](2) (18). The cationic [Ir(DMSO)(2)(DMSO)(2)]PF(6) complex (formed in situ from [Ir(coe)(2)(O=CMe(2))(2)]PF(6)) also reacts with methanol to give the hydrido-alkoxo complex syn-[(DMSO)(2)HIr(micro-OCH(3))(3)IrH(DMSO)(2)]PF(6) (19). Complexes 1, 2, 4, 5, 11, 12, 14, 17, 18, and 19 were characterized by crystallography.

Journal Article↗
PubMed1976

Interaction of apoprotein from porcine high-density lipoprotein with dimyristoyl lecithin. 1. The structure of the complexes.

The morphology and structural organisation of the complexes formed from the apoprotein of porcine high-density lipoprotein and dimyristoyl phosphatidylcholine (lecithin) have been studied using the technique of small-angle X-ray scattering. Scattering measurements made in solvents of varying electron density were interpreted in terms of a scattering-equivalent model for the structure of the complex. This model is described by an oblate ellipsoidal morphology with dimensions at 20 degrees C: major axis 11.0 nm, minor axis 5.5 nm. Within this overall shape the lipid hydrocarbon chains are organised in an apolar core whilst the lipid polar head groups and protein are located in a outer shell 0.85 nm in thickness. The oblate morphology demonstrates that the structure of the complex is directed by the fundamental bilayer organisation of the lecithin. The dimension of the minor axis (5.5 nm) indicates that phospholipid hydrocarbon chains are orientated perpendicular to the interface.

Animals↗
PubMed1990

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.

O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.

Alanine↗
PubMed1982

The effect of amine structure on complexation with lasalocid in model membrane systems. I. Identification of charged complexes in lipid bilayer membranes.

The electrical properties of X-537A (lasalocid) doped lipid bilayer membranes were studied in the presence of a series of nine biogenic amines which contain beta-phenylethylamine as the basic structural unit. The ionophore antibiotic was found to form charged complexes within the membrane during the transport of some of the amines. The dependence of membrane conductance on the concentration of ionophore and amine was studied. The amines are divided into three classes according to the nature of the complexes formed: (1) charged complex involving two ionophores (phenylephrine, metanephrine, and amphetamine); (2) charged complex containing three ionophores (dopamine, norepinephrine and epinephrine); and (3) no charged species formed (p- and m-tyramine and beta-phenylethylamine).

Biogenic Amines↗
PubMed1985

Structure of complex flagellar filaments in Rhizobium meliloti.

The complex flagella of Rhizobium meliloti 2011 and MVII-1 were analyzed with regard to serology, fine structure, subunits, and amino acid composition. The serological identities of flagellar filaments of the two strains were demonstrated by double immunodiffusion with antiflagellin antiserum. The filaments had a diameter of 16 nm. Their morphology was dominated by the prominent undulations of an external three-start helix running at a 10-nm axial distance and at an angle of 32 degrees. Faint nearly axial striations indicated the presence of a tubular core of a different helical order. The complex filaments consisted of 40,000-dalton flagellin monomers. Typically, the amino acid composition was 3 to 4% higher in nonpolar residues and 5 to 7% lower in aspartic and glutamic acids (and their amides) than that of plain flagellar proteins. There were no immunochemical relationships among Pseudomonas rhodos, Rhizobium lupini, and R. meliloti complex flagella, suggesting that the latter represent a new class.

Amino Acids↗
PubMed2005

Comparison of crystal structures of human type 3 3alpha-hydroxysteroid dehydrogenase reveals an "induced-fit" mechanism and a conserved basic motif involved in the binding of androgen.

The aldo-keto reductase (AKR) human type 3 3alpha-hydroxysteroid dehydrogenase (h3alpha-HSD3, AKR1C2) plays a crucial role in the regulation of the intracellular concentrations of testosterone and 5alpha-dihydrotestosterone (5alpha-DHT), two steroids directly linked to the etiology and the progression of many prostate diseases and cancer. This enzyme also binds many structurally different molecules such as 4-hydroxynonenal, polycyclic aromatic hydrocarbons, and indanone. To understand the mechanism underlying the plasticity of its substrate-binding site, we solved the binary complex structure of h3alpha-HSD3-NADP(H) at 1.9 A resolution. During the refinement process, we found acetate and citrate molecules deeply engulfed in the steroid-binding cavity. Superimposition of this structure with the h3alpha-HSD3-NADP(H)-testosterone/acetate ternary complex structure reveals that one of the mobile loops forming the binding cavity operates a slight contraction movement against the citrate molecule while the side chains of many residues undergo numerous conformational changes, probably to create an optimal binding site for the citrate. These structural changes, which altogether cause a reduction of the substrate-binding cavity volume (from 776 A(3) in the presence of testosterone/acetate to 704 A(3) in the acetate/citrate complex), are reminiscent of the "induced-fit" mechanism previously proposed for the aldose reductase, another member of the AKR superfamily. We also found that the replacement of residues Arg(301) and Arg(304), localized near the steroid-binding cavity, significantly affects the 3alpha-HSD activity of this enzyme toward 5alpha-DHT and completely abolishes its 17beta-HSD activity on 4-dione. All these results have thus been used to reevaluate the binding mode of this enzyme for androgens.

3-alpha-Hydroxysteroid Dehydrogenase (B-Specific)↗
PubMed1980

Structural analysis of electrical properties of cells and tissues.

Most cells and tissues have electrical properties relevant to their natural function. Most cells and tissues have rather complex structure, consisting of folding and invaginating membranes and specialized connections and organelles. The localization of electrical properties is particularly important, since each of the complex structures must be expected to have a specific role in the electrical function of the tissue. The structural analysis of electrical properties consists then in the measurements of the electrical properties of the individual components of the tissue or cell. The structural analysis proceeds by a qualitative analysis of the topology of the preparation, followed by quantitative measurements of the morphometric parameters, the surface, and volume of the relevant structures. A theoretical analysis is performed to determine the electrical properties expected from such a structure. Measurements of natural and induced electrical properties are then made. Comparison of the observed electrical properties with those predicted allows determination of the properties of individual components of the tissue. In this manner the role of individual membrane systems in the function of both skeletal muscle and the lens of the eye has been determined.

Cell Membrane Permeability↗
PubMed1996

Magnetic Susceptibility Trends in Oxo-Bridged, Dinuclear Chromium(III) Complexes. Crystal Structure of [(tmpa)Cr(&mgr;-O)(&mgr;-CO(3))Cr(tmpa)](ClO(4))(2).2H(2)O.

The synthesis and physical characterization of oxo-bridged [Cr(2)(tmpa)(2)(&mgr;-O)(X)](n)()(+) complexes (tmpa = tris(2-pyridylmethyl)amine) containing a variety of complementary ligands (X = CO(3)(2)(-), PhPO(4)(2)(-), HS(-)) are described, with the objective of understanding factors underlying variations in the antiferromagnetic coupling constant J. We also present the crystal structure of [(tmpa)Cr(&mgr;-O)(&mgr;-CO(3))Cr(tmpa)](ClO(4))(2).2H(2)O, for comparison with previous findings on [(tmpa)Cr(&mgr;-O)(&mgr;-CH(3)CO(2))Cr(tmpa)](ClO(4))(3). The carbonate-bridged complex crystallizes in the monoclinic space group P2(1)/c with a = 11.286(10) Å, b = 18.12(2) Å, c = 20.592(12) Å, beta = 95.99(5) degrees, and V = 4190 Å(3) and Z = 4. Asymmetric tmpa ligation pertains, with apical N atoms situated trans to bridging oxo and acido O atoms. Key structural parameters include Cr-O(b) bond lengths of 1.818(6) and 1.838(6) Å, Cr-OCO(2) distances of 1.924(7) and 1.934(7) Å, and a bridging bond angle of 128.3(3) degrees. Several attempts to prepare oxo, amido-bridged dimers were unsuccessful, but the nearlinear [Cr(tmpa)(N(CN)(2))](2)O(ClO(4))(2).3H(2)O complex was isolated from the reaction of dicyanamide ion with [Cr(tmpa)(OH)](2)(4+). In contrast to the behavior of analogous diiron(III) complexes, antiferromagnetic coupling constants of [Cr(2)(tmpa)(2)(&mgr;-O)(X)](n)()(+) dinuclear species are highly responsive to the X group. Considering the complexes with X = CO(3)(2)(-), PhPO(4)(2)(-), HS(-), SO(4)(2)(-), and RCO(2)(-) (10 R substituents), we find a reasonably linear, empirical relationship between J and oxo bridge basicity, as measured by pK(a) (Cr(OH)Cr) values in aqueous solution. While there is no theoretical basis for such a correlation between solid-state and solution-phase properties, this relationship demonstrates that CrOCr pi-bonding contributes significantly to antiferromagnetic exchange. Thus, J tends to become less negative with increasing &mgr;-O(2)(-) basicity, showing that greater availability of a bridging oxo group lone pair toward the proton, with decreasing CrOCr pi-interaction, reduces the singlet-triplet gap.

Journal Article↗
PubMed2001

Synthesis and reactivity of bridging and terminal hydrosulfido palladium and platinum complexes. Crystal structures of [NBu4]2[(Pt(c6F5)2(mu-SH)]2], [Pt(C6F5)2(PPh3)[S(H)AgPPh3]], and [Pt(C6F5)2(PPh3)[S(AuPPh3)2]].

The reactions of the hydroxo complexes [M(2)R(4)(mu-OH)(2)](2)(-) (M = Pd, R = C(6)F(5), C(6)Cl(5); M = Pt, R = C(6)F(5)), [[PdR(PPh(3))(mu-OH)](2)] (R = C(6)F(5), C(6)Cl(5)), and [[Pt(C(6)F(5))(2)](2)(mu-OH)(mu-pz)](2-) (pz = pyrazolate) with H(2)S yield the corresponding hydrosulfido complexes [M(2)(C(6)F(5))(4)(mu-SH)(2)](2-), [[PdR(PPh(3))(mu-SH)](2)], and [[Pt(C(6)F(5))(2)](2)(mu-SH)(mu-pz)](2-), respectively. The monomeric hydrosulfido complexes [M(C(6)F(5))(2)(SH)(PPh(3))](-) (M = Pd, Pt) have been prepared by reactions of the corresponding binuclear hydrosulfido complexes [M(2)(C(6)F(5))(4)(mu-SH)(2)](2-) with PPh(3) in the molar ratio 1:2, and they can be used as metalloligands toward Ag(PPh(3))(+) to form the heterodinuclear complex [(C(6)F(5))(2)(PPh(3))[S(H)AgPPh(3)]], and toward Au(PPh(3))(+) yielding the heterotrinuclear complexes [M(C(6)F(5))(2)(PPh(3))[S(AuPPh(3))(2)]]. The crystal structures of [NBu(4)](2)[[Pt(C(6)F(5))(2)(mu-SH)](2)], [Pt(C(6)F(5))(2)(PPh(3))[S(H)AgPPh(3)]], and [Pt(C(6)F(5))(2)(PPh(3))[S(AuPPh(3))(2)]] have been established by X-ray diffraction and show no short metal-metal interactions between the metallic centers.

Journal Article↗
PubMed2002

The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex.

Cre recombinase uses two pairs of sequential cleavage and religation reactions to exchange homologous DNA strands between 34 base-pair (bp) LoxP recognition sequences. In the oligomeric recombination complex, a switch between "cleaving" and "non-cleaving" subunit conformations regulates the number, order, and regio-specificity of the strand exchanges. However, the particular sequence of events has been in question. From analysis of strand composition of the Holliday junction (HJ) intermediate, we determined that Cre initiates recombination of LoxP by cleaving the upper strand on the left arm. Cre preferred to react with the left arm of a LoxP suicide substrate, but at a similar rate to the right arm, indicating that the first strand to be exchanged is selected prior to cleavage. We propose that during complex assembly the cleaving subunit preferentially associates with the LoxP left arm, directing the first strand exchange to that side. In addition, this biased assembly would enforce productive orientation of LoxP sites in the recombination synapses. A novel Cre-HJ complex structure in which LoxP was oriented with the left arm bound by the cleaving Cre subunit suggested a physical basis for the strand exchange order. Lys86 and Lys201 interact with the left arm scissile adenine base differently than in structures that have a scissile guanine. These interactions are associated with positioning the 198-208 loop, a structural component of the conformational switch, in a configuration that is specific to the cleaving conformation. Our results suggest that strand exchange order and site alignment are regulated by an "induced fit" mechanism in which the cleaving conformation is selectively stabilized through protein-DNA interactions with the scissile base on the strand that is cleaved first.

Attachment Sites, Microbiological↗
PubMed2001

Crystal structure at 2.8 A of an FcRn/heterodimeric Fc complex: mechanism of pH-dependent binding.

The neonatal Fc receptor (FcRn) transports immunoglobulin G (IgG) across epithelia, binding IgG in acidic vesicles (pH < or = 6.5) and releasing IgG in the blood at pH 7.4. Well-ordered FcRn/Fc crystals are prevented by the formation of "oligomeric ribbons" of FcRn dimers bridged by Fc homodimers, thus we crystallized a 1:1 complex between rat FcRn and a heterodimeric Fc containing only one FcRn binding site. The 2.8 A complex structure demonstrates that FcRn uses its alpha2 and beta2-microglobulin domains and carbohydrate to interact with the Fc C(gamma)2-C(gamma)3 interface. The structure reveals conformational changes in Fc and three titratable salt bridges that confer pH-dependent binding, and can be used to guide rational design of therapeutic IgGs with longer serum half-lives.

Animals↗
PubMed1997

ESR Studies of Oxochromium(V) Porphyrin Complexes: Electronic Structure of the Cr(V)=O Moiety.

ESR spectra of oxochromium(V) porphyrins were obtained to investigate the electronic structure of the Cr(V)=O moiety. At room temperature, the chlorooxochromium(V) meso-tetramesitylporphyrin complex 1-Cl exhibits an isotropic ESR signal, split into nine signals due to hyperfine coupling with four equivalent( 14)N, at g = 1.982. A small isotropic satellite signal, split into a quartet due to hyperfine coupling by the (53)Cr isotope is also observed. At 77 K, 1-Cl shows an anisotropic ESR signal with g( parallel) = 1.986 and g( perpendicular) = 1.980 and small satellite g( parallel) signals arising from hyperfine coupling with the (53)Cr isotope. The ESR parameters of 1-Cl, obtained from ESR spectral simulation, show that the pi-bonding character of the Cr(V)=O bond is not as strong as that of the Cr(V)&tbd1;N bond. To explore substituent effects on the bond character of the Cr(V)=O moiety, ESR spectra of perchloratooxochromium(V) porphyrins having various electronegative substituents were recorded. With an increase in electronegativity of the meso-substituent, the g( perpendicular) value and the (53)Cr hyperfine coupling constant (|a((53)Cr)|) are increased. These changes suggest an increase in the pi-bonding character of the Cr(V)=O moiety with an increase in the electronegativity of the meso-substituent. Furthermore, the hyperfine coupling constant of the oxo ligand, |a((17)O)|, obtained from ESR spectra of (17)O-labeled oxochromium(V) porphyrin is increased with an increase in electronegativity of the meso-substituent. This indicates that the radical character of the oxo ligand is increased by the electronegative meso-substituent. These data suggest that the pi-antibonding orbital of Cr=O is destabilized with an increase in electronegativity of the meso-substituent, which may facilitate bond breaking of the Cr=O moiety in an epoxidation reaction.

Journal Article↗
PubMed1989

Glycosylation of human leukocyte locus A molecules is dependent on the cell type.

Peripheral blood monocytes and B cells were isolated from a normal donor, and a portion of the B cells was transformed by the Epstein-Barr virus (EBV). Human leukocyte locus A (HLA) class-I and class-II molecules were immunoprecipitated by specific monoclonal antibodies after cell labeling with [3H]mannose. Glycopeptides of HLA molecules were obtained by pronase digestion and were analysed by lectin-affinity chromatography. Complex structures were hydrazinolysed, and their sialic acid content was analysed by ion-exchange chromatography, whereas the high-mannose structures were separated by HPLC. In normal cells, class-I antigens bear principally fucosylated biantennary structures while HLA-DR class-II antigens bear bi-, tri- and tetra-antennary structures and high-mannose structures. HLA antigens are more sialylated on normal B cells than on normal monocytes. An EBV cell line had a very different pattern of HLA-antigen glycosylation when compared with the original B cells. In the transformed cells, the fractions containing biantennary structures are largely decreased. In contrast, an increase of the tri- and tetra-antennary structure fractions is noticed, particularly in class-II molecules, while both triantennary and high-mannose structures are increased in class-I molecules. Moreover, when compared to normal B cells, the complex structures of class-I antigens in the EBV-transformed B-cell line are undersialylated while they are oversialylated in the case of the class-II molecules.

Antibodies, Monoclonal↗
PubMedDate not supplied

Early changes of experimentally induced cerebral aneurysms in rats: scanning electron microscopic study.

To obtain information about the early changes of experimentally induced cerebral aneurysms in rats, the luminal surface of branching areas of their cerebral arteries was examined with a scanning electron microscope. At the branching sites of major cerebral arteries in the control animals, the intima just distal to the apex markedly protruded into the lumen forming a linear bank-like intimal pad. Along and distal to this pad, there was a shallow long groove (juxta-apical groove). Such grooves were much deeper and wider in experimental animals than those in the control rats. By studying various stages of early aneurysmal changes, cerebral aneurysms were proven to develop from such grooves. In deep juxta-apical grooves and small aneurysms, round regenerated endothelial cells with a large number of microvilli were diffusely present. Degenerated cells with balloons and craters were observed intermingled with such regenerated cells. Interendothelial gaps were also seen. The present study showed the complex structure of the apex of arterial bifurcation in rats, including bank-like intimal pads. Such complex structures of the branching sites were considered to be responsible for the initiation of cerebral aneurysms due to endothelial injury possibly caused by turbulent flow there.

Animals↗
PubMed1995

2,6-diacetylpyridine bis(thiosemicarbazones) zinc complexes: synthesis, structure, and biological activity.

The reaction of zinc chloride, acetate, or perchlorate with two bis(thiosemicarbazones) of 2,6-diacetylpyridine [H2daptsc = 2,6-diacetylpyridine bis(thiosemicarbazone) and H2dapipt = 2,6-diacetylpyridine bis(hydrazinopyruvoylthiosemicarbazone)] leads to the formation of four novel complexes that have been characterized by spectroscopic studies (NMR, IR) and biological properties. The crystal structures of the two compounds--[Zn(daptsc)]2.2DMF (1) and [Zn(H2dapipt)(OH2)2](CIO4)2.3H2O (2)--also have been determined by x-ray methods from diffractometer data. Compound (1) is dimeric and the two zinc atoms have a distorted octahedral coordination. The ligand is deprotonated. In compound (2), the coordination geometry about zinc is pentagonal--bipyramidal and the ligand is in the neutral form. The molecular structure of (2) consists of cations [Zn(H2dapipt)(OH2)]2+, CIO4- disordered anions, and three water molecules of solvation. Biological studies have shown that the ligands and the complexes Zn(daptsc).1/2EtOH and Zn(H2daptsc)Cl2 have an effect in vitro on cell proliferation and differentiation (inhibition); both are concentration dependent. [Zn(daptsc)]2.2DMF (1) shows the effects at lower concentration values with respect to other compounds.

Cell Division↗
PubMed1994

Crystal structure of RNase T1 complexed with the product nucleotide 3'-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2'-hydroxyl group of the ribose.

The crystal structure of RNase T1 complexed with 3'-GMP has been determined. The glycosyl conformation of 3'-GMP is in the syn conformation, and the ribose adopts the O4'-endo pucker. This observed pucker is different from that in any complex structures of RNase T1. In the present complex, this energetically unfavorable conformation is stabilized by the water molecule with the bridged hydrogen bonds between the O2' and the O3' atoms of the ribose. The guanine base is recognized in the same manner as observed in the complex of 2'-GMP. The 2'-hydroxyl group of the ribose shows a tight hydrogen bond to both His-40 and Glu-58 with the suitable geometry for the proton transfer. These hydrogen bonds suggest that the two residues can participate directly in the proton transfer. His-92 is hydrogen bonded to two the proton transfer. His-92 is hydrogen bonded to two oxygen atoms of the phosphate group. Based on the geometry in the active site, the O1P atom may correspond to the O5' atom of the leaving nucleotide in the phosphoryl transfer or a water molecule as a nucleophile in the hydrolysis reaction. In the present complex, the conformations of the 3'-GMP molecule and the side chains of the catalytic residues would be represented as the conformation before the phosphoryl transfer reaction and/or after the hydrolysis reaction.

Binding Sites↗