title: Analysis of relative positions of ribonucleotide bases in a crystal structure of ribosome.
abstract: Relative positions of bases to bases in a crystal structure of ribosome were analyzed extensively. It was found that there is no clear relation between bases apart more than 15 A and, thus, the relative location of bases can be analyzed within 15 A of the reference bases. As for base pairing, major positioning was found to be due to the Watson-Crick type base pairs. Some other positions corresponding to non-Watson-Crick type base pairs were also found in some extents. As for base-base stacking, it was observed that the bases stacked to adenine base are dispersive. It was found that less non-Watson-Crick base pairs was found close to the protein binding site, suggesting that the protein components have a tendency to bind to the regular stem structures. The database of relative location of bases must be useful for improvement of structural determination and structural modeling systems.
authors.affiliation: Department of Industrial Chemistry, Faculty of Engineering, Chiba Institute of Technology, Narashino-shi, Japan.
authors.forename: Akitsugu
authors.initials: A
authors.lastname: Takasu
authors.forename: Kimitsuna
authors.initials: K
authors.lastname: Watanabe
authors.forename: Gota
authors.initials: G
authors.lastname: Kawai
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001665:Binding Sites; D003196:Computer Graphics; D003461:Crystallography; D016208:Databases, Factual; D019614:Haloarcula marismortui / Q000737:chemistry; D008958:Models, Molecular; D011485:Protein Binding; D011685:Purine Nucleotides / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012265:Ribonucleotides / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*; D015003:Yeasts / Q000737:chemistry
chemical_list: D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D012265:Ribonucleotides; D012313:RNA