Tetrahedral molecular geometry
About: Tetrahedral molecular geometry is a(n) research topic. Over the lifetime, 1795 publication(s) have been published within this topic receiving 30706 citation(s).
Papers published on a yearly basis
07 May 1980-Journal of Molecular Biology
TL;DR: The structure of bovine erythrocyte Cu, Zn superoxide dismutase has been determined to 2 A resolution using only the larger structure factors beyond 4 A and stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry.
Abstract: The structure of bovine erythrocyte Cu, Zn superoxide dismutase has been determined to 2 A resolution using only the larger structure factors beyond 4 A. The enzyme crystallizes in space group C2 with two dimeric enzyme molecules per asymmetric unit. All four crystallographically independent subunits were fitted separately to the electron density map at 2 A resolution on the University of North Carolina GRIP-75 molecular graphics system. Atomic co-ordinates were refined using the Hendrickson & Konnert (1980) program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 25.5% with a root-mean-square deviation of 0.03 A from ideal bond lengths and an average atomic temperature factor of 12 A2. Each enzyme subunit is composed primarily of eight antiparallel β strands that form a flattened cylinder, plus three external loops. The β barrel is asymmetrical and can be viewed as having two distinct sides; β strands 5 to 8 are shorter with fewer hydrogen bonds, less regular side-chain alternation, and greater twist than strands 1 to 4. The main-chain hydrogen bonds primarily link β strand residues; side-chain to main-chain hydrogen bonds are extensively involved in the formation of tight turns, which form a major structural element of the three loops. The largest loop includes both a disulfide region and a Zn-liganding region, each of which resembles one of the other two loops in overall structure. The second largest loop includes a short section of α helix. The smallest loop forms a Greek key connection across one end of the β barrel. The single disulfide bond, which forms a left-handed spiral, covalently joins the largest loop to the beginning of β strand 8. Symmetrically related β bulge pairs fold the two large loops back against the external surface of the β barrel to surround the active channel. The active site Cu(II) and Zn(II) lie 6.3 A apart at the bottom of this long channel; the Zn is buried, while the Cu is solvent-accessible. The side-chain of His61 forms a bridge between the Cu and Zn and is coplanar with them within the current accuracy of the data. The Cu ligands ND1 of His44 and NE2 of His46, −61 and −118 show an uneven tetrahedral distortion from a square plane. The Cu has a fifth axial coordination position exposed to solvent. Zn ligands ND1 of His61, −69 and −78 and OD1 of Asp81 show tetrahedral geometry with a strong distortion toward a trigonal pyramid having the buried Asp81 at the apex. Both the side-chains and mainchains of the metal-liganding residues are stabilized in their orientation by a complex network of hydrogen bonds.
14 Mar 2007
TL;DR: The structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure–factor least‐squares refinement at 2.0 Å resolution and some of the hydrogen bond donor–acceptor relations in the active site can be assigned.
Abstract: The structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure–factor least-squares refinement at 2.0 A resolution. The conventional crystallographic R value is 17.3%. Of 167 solvent molecules associated with the protein, four are buried and stabilize secondary structure elements. The zinc ion is ligated to three histidyl residues and one water molecule in a nearly tetrahedral geometry. In addition to the zinc-bound water, seven more water molecules are identified in the active site. Assuming that Glu-106 is deprotonated at pH 8.5, some of the hydrogen bond donor–acceptor relations in the active site can be assigned and are described here in detail. The Oγ1 atom of Thr-199 donates its proton to the Oe1 atom of Glu-106 and can function as a hydrogen bond acceptor only in additional hydrogen bonds.
01 Jan 2000-Chemistry of Materials
TL;DR: In this paper, three 8-hydroxyquinolato (q) boron compounds B(C2H5)2q (1), BPh2q 2q (2), and B(2-naph)2qs (3) have been synthesized by the reaction of 8-oxoquinoline with an appropriate BR3 compound, and their electroluminescent properties were examined by fabricating EL devices using 2 and 3 as the light emitting layer, respectively.
Abstract: Three 8-hydroxyquinolato (q) boron compounds B(C2H5)2q (1), BPh2q (2), and B(2-naph)2q (3) have been synthesized by the reaction of 8-hydroxyquinoline with an appropriate BR3 compound. Compounds 1−3 have a tetrahedral geometry as demonstrated by the structure of 1 determined by a single-crystal X-ray diffraction analysis. Compounds 1−3 emit a green-blue color at λmax = 495−500 nm when irradiated by UV light. The electroluminescent (EL) properties of 2 and 3 were examined by fabricating EL devices using 2 and 3 as the light-emitting layer, respectively. The devices of 2 produce a yellow-green light with broad emission spectra, attributed to the formation of an exciplex of 2 with the N,N‘-di-1-naphthyl-N,N‘-diphenylbenzidine (NPB) in the hole transport layer while the intrinsic EL emission of compound 3 was observed. Both 2 and 3 were found to be good electron transport materials in EL devices.
15 Jan 1987-Journal of Molecular Biology
TL;DR: The structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined, using counter data recorded from crystals at pH 3.8 and 7.8, and the trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive.
Abstract: The structure of poplar plastocyanin in the reduced (CuI) state has been determined and refined, using counter data recorded from crystals at pH 3.8, 4.4, 5.1, 5.9, 7.0 and 7.8 (resolution 1.9 A, 1.9 A, 2.05 A, 1.7 A, 1.8 A and 2.15 A; the final residual R value was 0.15, 0.15, 0.16, 0.17, 0.16 and 0.15, respectively). The molecular and crystal structure of the protein is substantially the same in the reduced state as in the oxidized state. The refinements of the structures of the six forms of the reduced protein could therefore be commenced with a model derived from the known structure of CuII-plastocyanin. The refinements were made by reciprocal space least-squares calculations interspersed with inspections of electron-density difference maps. Precautions were taken to minimize any bias of the results of the refinements in the direction of the starting model. The most significant differences among the structures of the reduced protein at the six pH values, or between them and the structure of the oxidized protein, are concentrated at the Cu site. In the reduced protein at high pH (pH 7.8), the CuI atom is co-ordinated by the N delta(imidazole) atoms of His37 and His87, the S gamma(thiolate) atom of Cys84, and the S delta(thioether) atom of Met92, just as in CuII-plastocyanin. The distorted tetrahedral geometry and the unusually long Cu-S(Met92) bond are retained. The only effects of the change in oxidation state are a lengthening of the two Cu-N(His) bonds by about 0.1 A, and small changes in two bond angles involving the Cu-S(Cys) bond. The high-pH form of reduced plastocyanin accordingly meets all the requirements for efficient electron transfer. As the pH is lowered, the Cu atom and the four Cu-binding protein side-chains appear to undergo small but concerted movements in relation to the rest of the molecule. At low pH (pH 3.8), the CuI atom is trigonally co-ordinated by N delta(His37), S gamma(Cys84) and S delta(Met92). The fourth Cu-ligand bond is broken, the Cu atom making only a van der Waals' contact with the imidazole ring of His87. The trigonal geometry of the Cu atom strongly favours CuI, so that this form of the protein should be redox-inactive. This is known to be the case.(ABSTRACT TRUNCATED AT 400 WORDS)
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