erium 7. Protein structure. Examine the three-dimensional atomic structure of th
ID: 192764 • Letter: E
Question
erium 7. Protein structure. Examine the three-dimensional atomic structure of the protein EF-G-2 from the bact Thermus thermophilus. Find the atomic coordinates of the crystal structure of this protein http://www.resb.org/pdb/home/home.do. Look for the file name called 2DYI. Visualize the structure using Jmol software (http://bioinformatics.org/firstglance/fgij/). Answer the following questions. at A) How many amino acid residues are in EF-G-2? B) What is the resolution of the crystal structure? C) What ligand is bound to EF-G-2? D) Describe the topology of domain 3 of EF-G-2. How many -helices and -strands? Are the -strands parallel or anti-parallel? What neighboring domains interact non-covalently with domain 3? E) Find the amino acid residue Glul87. This residue makes electrostatic interactions with residue. F) Find Lys469. In what type of secondary structure is this residue? This residue makes hydrogen bonds with residue which residues are part of -turns? [Circle the numbers corresponding to these residues.] 415 417 419 421 G) 4 H) Which residues are part of the hydrophobic core of EF-G-2? [Circle the mumbers corresponding to these residues.] 402 403 406 407Explanation / Answer
Ans A) 658 amino acid residues in GF-G-2 protein of thermus thermophilus.
Ans B) Resolution: 1.6 Å
AnsC) Mg701:A and GTP700:A residues are present.
Ans D)
33% helical (25 helices; 220 residues)
33% beta sheet (39 strands; 223 residues)
Y tyrosin
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