Human Carboxyhemoglobin at 2.2 Å Resolution: Structure and Solvent Comparisons of R-State, R2-State and T-State Hemoglobins

1998 ◽  
Vol 54 (3) ◽  
pp. 355-366 ◽  
Author(s):  
Gregory B. Vásquez ◽  
Xinhua Ji ◽  
Clara Fronticelli ◽  
Gary L. Gilliland
Keyword(s):  
Water Molecule ◽  
Three Dimensional ◽  
Water Structure ◽  
Crystal Form ◽  
Dimensional Structure ◽  
Α Subunit ◽  
Phosphate Ion ◽  
Significant Difference ◽  
Chain Conformations ◽  
T State

The three-dimensional structure and associated solvent of human carboxyhemoglobin at 2.2 Å resolution are compared with other R-state and T-state human hemoglobin structures. The crystal form is isomorphous with that of the 2.7 Å structure of carboxyhemoglobin reported earlier [Baldwin (1980). J. Mol. Biol. 136, 103–128], whose coordinates were used as a starting model, and with the 2.2 Å structure described in an earlier report [Derewenda et al. (1990). J. Mol. Biol. 211, 515–519]. During the course of the refinement, a natural mutation of the α-subunit, A53S, was discovered that forms a new crystal contact through a bridging water molecule. The protein structure shows a significant difference between the α and β heme geometries, with Fe—C—O angles of 125 and 162°, respectively. The carboxyhemoglobin is compared with other fully ligated R-state human hemoglobins [Baldwin (1980). J. Mol. Biol. 136, 103–128; Shaanan (1983). J. Mol. Biol. 195, 419–422] with the R2-state hemoglobin [Silva et al. (1992). J. Biol. Chem. 267, 17248–17256] and with T-state deoxyhemoglobin [Fronticelli et al. (1994). J. Biol. Chem. 269, 23965–23969]. The structure is similar to the earlier reported R-state structures, but there are differences in many side-chain conformations, the associated water structure and the presence and the position of a phosphate ion. The quaternary changes between the R-state carboxyhemoglobin and the R2-state and T-state structures are in general consistent with those reported in the earlier structures. The location of 238 water molecules and a phosphate ion in the carboxyhemoglobin structure allows the first comparison of the solvent structures of the R-state and T-state structures. Distinctive hydration patterns for each of the quaternary structures are observed, but a number of conserved water molecule binding sites are found that are independent of the conformational state of the protein.

scholarly journals Poly[[tetraaquabis(μ3-5-carboxybenzene-1,2,4-tricarboxylato)tricadmium] tetrahydrate]

2012 ◽  
Vol 68 (6) ◽  
pp. m801-m802
Author(s):  
Yong-Yan Jia ◽  
Xin-Nian Xie ◽  
Huai-Xia Yang
Keyword(s):  
Water Molecule ◽  
Three Dimensional ◽  
Octahedral Geometry ◽  
Title Complex ◽  
Dimensional Structure ◽  
Distorted Octahedral Geometry ◽  
Water Molecules ◽  
Three Dimensional Structure ◽  
The Third ◽  
Distorted Octahedral

There are three independent CdII ions in the title complex, {[Cd3(C10H3O8)2(H2O)4]·4H2O} n , one of which is coordinated by four O atoms from three 5-carboxybenzene-1,2,4-tricarboxylate ligands and by two water molecules in a distorted octahedral geometry. The second CdII ion is coordinated by five O atoms from four 5-carboxybenzene-1,2,4-tricarboxylate ligands and by one water molecule also in a distorted octahedral geometry while the third CdII ion is coordinated by five O atoms from three 5-carboxybenzene-1,2,4-tricarboxylate ligands and by one water molecule in a highly distorted octahedral geometry. The 5-carboxybenzene-1,2,4-tricarboxylate ligands bridge the CdII ions, resulting in the formation of a three-dimensional structure. Intra- and intermolecular O—H...O hydrogen bonds are present throughout the three-dimensional structure.

scholarly journals Preliminary crystallographic analysis of Xyn52B2, a GH52 β-D-xylosidase fromGeobacillus stearothermophilusT6

2014 ◽  
Vol 70 (12) ◽  
pp. 1675-1682 ◽  
Author(s):  
Roie Dann ◽  
Shifra Lansky ◽  
Noa Lavid ◽  
Arie Zehavi ◽  
Valery Belakhov ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Crystal Form ◽  
Thermophilic Bacterium ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
Glycoside Hydrolase Family ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Cell Parameters ◽  
Average Unit

Geobacillus stearothermophilusT6 is a thermophilic bacterium that possesses an extensive hemicellulolytic system, including over 40 specific genes that are dedicated to this purpose. For the utilization of xylan, the bacterium uses an extracellular xylanase which degrades xylan to decorated xylo-oligomers that are imported into the cell. These oligomers are hydrolyzed by side-chain-cleaving enzymes such as arabinofuranosidases, acetylesterases and a glucuronidase, and finally by an intracellular xylanase and a number of β-xylosidases. One of these β-xylosidases is Xyn52B2, a GH52 enzyme that has already proved to be useful for various glycosynthesis applications. In addition to its demonstrated glycosynthase properties, interest in the structural aspects of Xyn52B2 stems from its special glycoside hydrolase family, GH52, the structures and mechanisms of which are only starting to be resolved. Here, the cloning, overexpression, purification and crystallization of Xyn52B2 are reported. The most suitable crystal form that has been obtained belonged to the orthorhombicP212121space group, with average unit-cell parametersa = 97.7,b= 119.1,c = 242.3 Å. Several X-ray diffraction data sets have been collected from flash-cooled crystals of this form, including the wild-type enzyme (3.70 Å resolution), the E335G catalytic mutant (2.95 Å resolution), a potential mercury derivative (2.15 Å resolution) and a selenomethionine derivative (3.90 Å resolution). These data are currently being used for detailed three-dimensional structure determination of the Xyn52B2 protein.

scholarly journals Coordination polymeric structures in the sodium salt of 4-chloro-3-nitrobenzoic acid and the sodium and potassium salts of 4-nitroanthranilic acid

2013 ◽  
Vol 69 (12) ◽  
pp. 1472-1477 ◽  
Author(s):  
Graham Smith
Keyword(s):  
Hydrogen Bonding ◽  
Water Molecule ◽  
Coordination Polyhedron ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Π Interactions ◽  
Nitrobenzoic Acid ◽  
Distorted Octahedral ◽  
Polymeric Structures

The structures of the hydrated sodium salts of 4-chloro-3-nitrobenzoic acid {poly[aqua(μ4-4-chloro-3-nitrobenzoato)sodium(I)], [Na(C7H3ClNO4)(H2O)]n, (I)} and 2-amino-4-nitrobenzoic acid {poly[μ-aqua-aqua(μ3-2-amino-4-nitrobenzoato)sodium(I)], [Na(C7H5N2O4)(H2O)2]n, (II)}, and the hydrated potassium salt of 2-amino-4-nitrobenzoic acid {poly[μ-aqua-aqua(μ5-2-amino-4-nitrobenzoato)potassium(I)], [K(C7H5N2O4)(H2O)]n, (III)} have been determined and their complex polymeric structures described. All three structures are stabilized by intra- and intermolecular hydrogen bonding and strong π–π ring interactions. In the structure of (I), the distorted trigonal bipyrimidal NaO5coordination polyhedron comprises a monodentate water molecule and four bridging carboxylate O-atom donors, generating a two-dimensional polymeric structure lying parallel to (001). Intra-layer hydrogen-bonding associations and strong inter-ring π–π interactions are present. Structure (II) has a distorted octahedral NaO6stereochemistry, with four bridging O-atom donors, two from a single carboxylate group and two from a single nitro group and three from the two water molecules, one of which is bridging. Na centres are linked through centrosymmetric four-membered duplex water bridges and through 18-membered duplex head-to-tail ligand bridges. Similar centrosymmetric bridges are found in the structure of (III), and in both (II) and (III) strong inter-ring π–π interactions are found. A two-dimensional layered structure lying parallel to (010) is generated in (II), whereas in (III) the structure is three-dimensional. With (III), the irregular KO7coordination polyhedron comprises a doubly bridging water molecule, a single bidentate bridging carboxylate O-atom donor and three bridging O-atom donors from the two nitro groups. A three-dimensional structure is generated. These coordination polymer structures are among the few examples of metal complexes of any type with either 4-chloro-3-nitrobenzoic acid or 4-nitroanthranilic acid.

scholarly journals Crystal structure of zwitterionic 4-(ammoniomethyl)benzoate: a simple molecule giving rise to a complex supramolecular structure

2014 ◽  
Vol 70 (11) ◽  
pp. 385-388 ◽  
Author(s):  
Ana María Atria ◽  
Maria Teresa Garland ◽  
Ricardo Baggio
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Compound C ◽  
Acidic Proton ◽  
Centroid Distance ◽  
Benzene Rings

The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammoniomethyl)benzoate zwitterion derived from 4-aminomethylbenzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15). In the crystal structure, N—H...O hydrogen bonds together with π–π stacking of the benzene rings [centroid–centroid distance = 3.8602 (18) Å] result in a strongly linked, compact three-dimensional structure.

Crystallization

2015 ◽  
Author(s):  
Roger G. Harrison ◽  
Paul W. Todd ◽  
Scott R. Rudge ◽  
Demetri P. Petrides
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Crystal Form ◽  
Solid Particles ◽  
Dimensional Structure ◽  
Internal Quality ◽  
Small Scale ◽  
X Ray Diffraction ◽  
Production Scale ◽  
Homogeneous Phase

Crystallization is the process of producing crystals from a homogeneous phase. For biochemicals, the homogeneous phase from which crystals are obtained is always a solution. Crystallization is similar to precipitation in that solid particles are obtained from a solution. However, precipitates have poorly defined morphology, while in crystals the constituent molecules are arranged in three-dimensional arrays called space lattices. In comparison to crystallization, precipitation occurs at much higher levels of supersaturation and rates of nucleation but lower solubilities. These and other differences between crystallization and precipitation are highlighted in Table 9.1. Because of these differences and because the theory of crystallization that has been developed is different from that for precipitation, crystallization is considered separately from precipitation. Crystallization is capable of producing bioproducts at very high purity (say, 99.9%) and is considered to be both a polishing step and a purification step. Polishing refers to a process needed to put the bioproduct in its final form for use. For some bioproducts, such as antibiotics, this final form must be crystalline, and sometimes it is even necessary that a specific crystal form be obtained. In some instances, the purification that can be achieved by crystallization is so significant that other more expensive purification steps such as chromatography can be avoided. There are actually two very different applications of crystallization in biotechnology and bioproduct engineering: crystallization for polishing and purification, and crystallization for crystallography. In the latter case, the goal is a small number of crystals with good size (0.2–0.9 mm) and internal quality. Although it has become common to crystallize proteins for characterization of their three-dimensional structure by x-ray diffraction, this is performed only at small scale in the laboratory, and the knowledge about how to crystallize proteins at large scale in a production process is less developed. However, many antibiotics and other small biomolecules are routinely crystallized in production scale processes. This chapter is oriented toward the use of crystallization in processes that can be scaled up.

scholarly journals A peptide mimic of an antigenic loop of α-human chorionic gonadotropin hormone: solution structure and interaction with a llama VHH domain

2002 ◽  
Vol 366 (2) ◽  
pp. 415-422 ◽  
Author(s):  
Gilles FERRAT ◽  
Jean-Guillaume RENISIO ◽  
Xavier MORELLI ◽  
Jerry SLOOTSTRA ◽  
Rob MELOEN ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chorionic Gonadotropin ◽  
Human Chorionic Gonadotropin ◽  
Solution Structure ◽  
Three Dimensional ◽  
Conformational Exchange ◽  
Dimensional Structure ◽  
Single Chain ◽  
Α Subunit ◽  
Human Chorionic Gonadotropin Hormone

The X-ray structure of a ternary complex between human chorionic gonadotropin hormone (hCG) and two Fvs recognizing its α and β subunits has been recently determined. The Fvs recognize the elongated hCG molecule by its two ends, one being the Leu-12–Cys-29 loop of the α subunit. We have designed and synthesized a 17-amino-acid peptide (named PepH14) derived from the sequence of this antigenic loop with the purpose of mimicking its three-dimensional structure and its affinity for antibodies. We have determined the solution structure of PepH14 by homonuclear NMR spectroscopy and derived distance restraints. Comparison of this structure with that of the corresponding antigenic loop of α-hCG reveals strong conformational similarities. In particular, the two pairs of residues that establish crucial contacts with the Fv fragment share the same conformation in PepH14 and in the authentic hormone loop. We propose a three-dimensional model of interaction of PepH14 with a llama VHH (VHH-H14) fragment cloned from a single-chain llama immunoglobulin raised against α-hCG. This model has been constrained by the chemical shift variations of the H14 1HN and 15N resonances monitored upon binding with PepH14. Mapping of the backbone chemical shift variations on the VHH structure determined by NMR indicates that PepH14 binds to VHH-H14 and forms a complex using the three complementary determining regions (CDRs). They define a shallow groove encompassing residues Thr-31, Ala-56, Tyr-59 and Trp-104 which have been shown to be in conformational exchange [Renisio, Pérez, Czisch, Guenneugues, Bornet, Frenken, Cambillau and Darbon (2002) Proteins 47, 546–555] and also Phe-37 and Ala-50. This groove is close to the hydrophobic interface area observed between VH and VL domains in Fvs from classical antibodies, which explains the rather lateral binding of PepH14 on the VHH.

scholarly journals Crystal structure of 1H,1′H-[2,2′-biimidazol]-3-ium hydrogen tartrate hemihydrate

2014 ◽  
Vol 70 (11) ◽  
pp. o1221-o1222 ◽  
Author(s):  
Xiao-Li Gao ◽  
Li-Fang Bian ◽  
Shao-Wei Guo
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Dihedral Angle ◽  
Rotation Axis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Hydrated Salt ◽  
Imidazolium Ring ◽  
Tartrate Anion

In the crystal of the title hydrated salt, C6H7N4+·C4H5O6−·0.5H2O, the biimidazole monocation, 1H,1′H-[2,2′-biimidazol]-3-ium, is hydrogen bonded,viaN—H...O, O—H...O and O—H...N hydrogen bonds, to the hydrogen tartrate anion and the water molecule, which is located on a twofold rotation axis, forming sheets parallel to (001). The sheets are linkedviaC—H...O hydrogen bonds, forming a three-dimensional structure. There are also C=O...π interactions present [O...π distances are 3.00 (9) and 3.21 (7) Å], involving the carbonyl O atoms and the imidazolium ring, which may help to consolidate the structure. In the cation, the dihedral angle between the rings is 11.6 (2)°.

Studies of structure and specificity of some antigen-antibody complexes

1989 ◽  
Vol 323 (1217) ◽  
pp. 487-494
Keyword(s):  
Monoclonal Antibodies ◽  
Three Dimensional ◽  
High Specificity ◽  
Single Amino Acid ◽  
Dimensional Structure ◽  
X Ray ◽  
Homologous Antigen ◽  
Significant Difference ◽  
Antigen Antibody ◽  
Antibody Interactions

By using X -ray diffraction and immunochemical techniques, we have exploited the use of monoclonal antibodies raised against hen egg lysozyme (HEL) to study systematically those factors responsible for the high specificity of antigen -antibody interactions. HEL was chosen for our investigations because its three-dimensional structure and immunochemistry have been well characterized and because naturally occurring sequence variants from different avian species are readily available to test the fine specificity of the antibodies. The X-ray crystal structure of a complex formed between HEL and the Fab D1.3 shows a large complementary surface with close interatomic contacts between antigen and antibody. Thus single amino acid sequence changes in heterologous antigens give antigen-antibody association constants that are several orders of magnitude smaller than that of the homologous antigen. For example, a substitution of His for Glu at position 121 in the antigen is sufficient to diminish significantly the binding between D1.3 and the variant lysozyme. The conformation of HEL when complexed to D1.3 shows no significant difference from that seen in the free molecule, and immunobinding studies with other anti-HEL antibodies suggest that this observation may be generally true for the system of monoclonal antibodies that we have studied.

Aqua(8-hydroxy-7-iodoquinoline-5-sulfonato-κ2 N,O 8)silver(I) dihydrate

2006 ◽  
Vol 62 (5) ◽  
pp. m1036-m1037 ◽  
Author(s):  
Hai-Yan Liu ◽  
Hua Wu ◽  
Jian-Fang Ma
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Water Molecule ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Intermolecular Hydrogen Bonding ◽  
Three Dimensional Structure ◽  
Sulfonate Anion

In the title compound, [Ag(C9H5INO4S)(H2O)]·2H2O, the AgI cation has a highly distorted trigonal–planar coordination geometry, with N and O donor atoms from a bidentate 8-hydroxy-7-iodoquinoline-5-sulfonate anion ligand and one O atom from a water molecule. In the crystal structure, the molecules are linked together through extensive intermolecular hydrogen bonding, forming a three-dimensional structure.

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