Nucleotide/protein sets

There are many high-resolution purine-nucleotide/protein co-crystal structures in the Protein Data Bank. Twenty six complex domains with a resolution < 2.50A were used these contained 13 ADP molecules, 10 ATP molecules and 3 mimics. Multimeric complexes were reduced to a single representative example site to avoid biasing the dataset. The sets of complete residues within 4.5A of the Van der Waals surface of each ligand were defined as the ligand binding sites and their co-ordinates extracted similarly from each complex. 

Codon (Section 28.11) Set of three successive nucleotides in mRNA that is unique for a particular amino acid. The 64 codons possible from combinations of A, T, G, and C code for the 20 amino acids from which proteins are constructed. 

Lefkowitz, R. J., Cotecchia, S., Samama, P. 8r Costa, T. (1993). Constitutive activity of receptors coupled to guanine nucleotide regulatory proteins. Trends Pharmacol Set 14, 303-7. 

In principle, phylogenetic trees may be generated from any data set that contains phylogenetic information. This chapter, however, is confined to nucleotide and amino acid sequences. These are the most widely used sources of molecular information for phylogenetic studies of species or higher taxa such as families or orders, and the phylogeny of proteins is an important and useful pursuit in its own right. To make a tree... 

Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (codon, terminator). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, transfer) complementary to all codons. These codons are referred to as unassigned codons (codons, nonsense). [NIH]... 

In essence, tRNA has two active sites one that is specific for a given amino acid and the other that is specific for a given set of three bases. The tRNA collects an appropriate amino acid and brings it to the growing polypeptide chain inserting it as directed by the mRNA. There is then a collinear relationship between the nucleotide base sequence of a gene and the amino acid sequence in the protein. 

The genetic code is a set of words or codons that are read as the nucleotide sequence of the mRNA and translated into the protein sequence it specifies. 

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