Question

The Question just states what I have given in terms of coordinates but I do believe it's related to the shape I assume. (Angles, size, ect.)

(a.) Obtain coordinates for: ATP, phosphatidylcholine, B-DNA. G-actin, the lambda represssor/DNA complex or Lac repressor/DNA complex, hemoglobin, myoglobin, HIv gp120, green fluorescent protein (GFP, and RNA polymerase.

(b.) Using a structural viewing code like VMD, create a plot of each of the molecules from part (a)​. Their coordinates can be obtained through their PDB File, a simple google search should help you find them.

(c) By looking at phosphatidylcholine, justify and find the value of the area per lipid.

(d) Phosphoglycerate kinase is a key enzyme in the glycolysis pathway. Obtain the coordinates for bth phosphoglycerate kinase and glucose and examine the relative size of the molecules.

Answer 1

To determine the molecular structure, using X-ray diffraction is most common technique.If the structure not determines by this method then for automatic validation of structure coordinate file generated.That contain information of unit cell that covers the molecules. It defines the the angle and distance of all the elements.

Coordinate obtain for various molecules listed here

Name. Length. (A^o) Angle (^o)

a. b. c.           

1. ATP.   132.540.   132.540. 110.500. 90.00.   90.00.   120.00
2. Phosphatidylcholine. 43.914. 73.773. 48.185. 90.00 114.73. 90.00
3. B-DNA.   63.710. 24.556   40.631. 90.00. 122.59. 90.00
4. G-actin.   95.731. 95.731.   96.948. 90.00. 90.00. 120.00
5. The lambda repressor/DNA.   150.900. 64.500.   27.800. 90.00. 90.00. 90.00
6. Hemoglobin.   62.650.   82.430.   53.530. 90.00. 99.61. 90.00
7. Myoglobin   63.800.   30.810.   34.350. 90.00. 105.80. 90.00
8. Hlv.   137.131.   179.697. 97.068. 90.00. 90.00. 90.00
9. GFP. 51.235.   62.350.   71.067. 90.00. 90.00. 90.00
10. RNA polymerase 220.200. 395.700.   282.100. 90.00. 90.00. 90.00