scholarly journals Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

2017 ◽  
Vol 73 (4) ◽  
pp. 316-325 ◽  
Author(s):  
Heping Zheng ◽  
Karol M. Langner ◽  
Gregory P. Shields ◽  
Jing Hou ◽  
Marcin Kowiel ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Structural Data ◽  
Bond Valence ◽  
Oxidation States ◽  
Experimental Crystal ◽  
Nitrogen Bonds ◽  
Almost All ◽  
Bond Valence Model

The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valenceR0parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal–organic bond-valence parameters.R0bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost allR0bond-valence parameters were reproduced, except for iron–nitrogen bonds, for which distinctR0parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.

scholarly journals Molecular dynamics simulations of zfP2X4 receptors

2021 ◽  
Author(s):  
kalyan immadisetty ◽  
Peter Kekenes-Huskey
Keyword(s):  
Molecular Dynamics ◽  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Pain Perception ◽  
Gulf Coast ◽  
Md Simulations ◽  
P2x Receptor ◽  
Metal Binding Sites

The ATP activated P2X4 receptor plays a prominent role in pain perception and modulation and thus may constitute an alternative therapeutic target for controlling pain. Given the biomedical relevance of P2X4 receptors, and poor understanding of molecular mechanisms that describe its gating by ATP, a fundamental understanding of the functional mechanism of these channels is warranted. Through classical all-atom molecular dynamics (MD) simulations we investigated the number of ATP molecules required to open (activate) the receptor for it to conduct ions. Since crystal structures of human P2X4 are not yet available, the crystal structures of highly-homologous zebrafish P2X4 (zfP2X4) structures were utilized for this study. It has been identified that at least two ATP molecules are required to prevent the open state receptor from collapsing back to a closed state. Additionally, we have discovered two metal binding sites, one at the intersection of the three monomers in the ectodomain (MBS1) and the second one near the ATP binding site (MBS2), both of which are occupied by the potassium ions. This observation draws its comparison to the gulf coast P2X receptor that it possesses the same two metal binding sites, however, MBS1 and MBS2 in this receptor are occupied by zinc and magnesium, respectively.

scholarly journals Crystal Structures of Apo and Metal-Bound Forms of the UreE Protein fromHelicobacter pylori: Role of Multiple Metal Binding Sites,

Biochemistry ◽  
2010 ◽  
Vol 49 (33) ◽  
pp. 7080-7088 ◽  
Author(s):  
Rong Shi ◽  
Christine Munger ◽  
Abdalin Asinas ◽  
Stéphane L. Benoit ◽  
Erica Miller ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Binding Sites

The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins

2014 ◽  
Vol 70 (7) ◽  
pp. 1823-1831 ◽  
Author(s):  
Nobutaka Numoto ◽  
Taro Nakagawa ◽  
Ryota Ohara ◽  
Tomoyo Hasegawa ◽  
Akiko Kita ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Metal Binding ◽  
Binding Sites ◽  
Structural Changes ◽  
Divalent Cations ◽  
Glycosylation Site ◽  
Metal Binding Sites ◽  
Molecular Masses ◽  
Quaternary Structures ◽  
Intersubunit Interactions

The quaternary structures of invertebrate haemoglobins (Hbs) are quite different from those of vertebrate Hbs. The extracellular giant Hbs of molecular masses of about 400 and 3600 kDa are composed of a dome-shaped dodecameric subassembly which consists of four individual globin subunits. Several crystal structures of 400 kDa Hbs from annelids have been reported, including structures in oxygenated and partially unliganded states, but the structure of the fully deoxygenated state has not been reported. In the present study, crystal structures of V2Hb from the tube wormLamellibrachia satsumahave been determined in both the fully oxygenated and deoxygenated states. A glycosylation site and novel metal-binding sites for divalent cations were clearly observed with no intersubunit interactions in V2Hb. A comparison of the oxygenated and the deoxygenated forms of V2Hb reveals that the ternary- and quaternary-structural changes occur in a manner that maintains the molecularD3symmetry. These structures suggest that the mechanisms of quaternary-structural changes between the oxy and deoxy states for the giant Hbs are identical across species.

scholarly journals Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition

2021 ◽  
Author(s):  
Yuliana Yosaatmadja ◽  
Hannah T Baddock ◽  
Joseph A Newman ◽  
Marcin Bielinski ◽  
Angeline E Gavard ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Metal Binding ◽  
Catalytic Domain ◽  
Structural Data ◽  
Strand Break ◽  
Dna Hairpin ◽  
End Joining ◽  
Class Switch ◽  
Dna Double Strand Break ◽  
Non Homologous End Joining

Artemis (DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in DNA double-strand break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Consistently, Artemis deficiency leads to radiosensitive congenital severe immune deficiency (RS-SCID). Artemis belongs to a structural superfamily of nucleases that contain conserved metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. Here, we present crystal structures of the catalytic domain of wild type and variant forms of Artemis that cause RS-SCID Omenn syndrome. The truncated catalytic domain of the Artemis is a constitutively active enzyme that with similar activity to a phosphorylated full-length protein. Our structures help explain the basis of the predominantly endonucleolytic activity of Artemis, which contrast with the predominantly exonuclease activity of the closely related SNM1A and SNM1B nucleases. The structures also reveal a second metal binding site in its β-CASP domain that is unique to Artemis. By combining our structural data that from a recently reported structure we were able model the interaction of Artemis with DNA substrates. Moreover, co-crystal structures with inhibitors indicate the potential for structure-guided development of inhibitors.

Crystallochemical analysis of the crystal structure of PbGa2S4: the bond valence model

2016 ◽  
Vol 39 (0) ◽  
pp. 7-11
Author(s):  
А. Я. Штейфан ◽  
В. І. Сідей ◽  
І. І. Небола ◽  
І. П. Студеняк
Keyword(s):  
Crystal Structure ◽  
Bond Valence ◽  
Bond Valence Model ◽  
Crystallochemical Analysis

Radially π-Extended Pyrrole-Fused Azacoronene: A Series of Crystal Structures of HPHAC with Various Oxidation States

2021 ◽  
Vol 86 (5) ◽  
pp. 4290-4295 ◽  
Author(s):  
Yoshiki Sasaki ◽  
Masayoshi Takase ◽  
Nagao Kobayashi ◽  
Shigeki Mori ◽  
Keishi Ohara ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Oxidation States
Sign in / Sign up

Export Citation Format

Share Document