Protein structure. Examine the three-dimensional atomic structure of the protein

Question

Protein structure. Examine the three-dimensional atomic structure of the protein EF-G-2 from the bacterium Thermus thermophilus. Find the atomic coordinates of the crystal structure of this protein at http://www.rcsb.org/pdb/home/home.do . Look for the file name called 2DY1. Visualize the structure using Jmol software (http://bioinformatics.org/firstglance/fgij/ ). Answer the following questions. 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 a-helices and b-strands? Are the b-strands parallel or anti-parallel? What neighboring domains interact non-covalently with domain 3? E) Find the amino acid residue Glu187. 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 ________. G) Which residues are part of b-turns? [Circle the numbers corresponding to these residues.] 415 417 419 421 H) Which residues are part of the hydrophobic core of EF-G-2? [Circle the numbers corresponding to these residues.] 402 403 406 407

Explanation / Answer

A. 665amino acids in EF-G-2

B. Resolution is the smallest distance between crystal lattice planes that is resolved in the differection pattern

C.  

D. In which 5domians are present

E. Histone H4 peptides are glu187 resides

F. Makes hydrogen bonds with Asp467

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