iCn3D Mutation Analysis
Author: Alexa M. Salsbury, PhD
iCn3D Shortcuts and Help Docs
1. Go to 1TUP(MMDB) in iCn3D
Note: you can use your previous rendering or start fresh
2. Click on Select > by Distance
![Screenshot from the iCn3D website, Select > by distance](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image002.png)
3. Choose nucleotides, set sphere radius to 3.5 Å, choose 1TUP_B, and click on Display
![Screenshot from the iCn3D website, Select a sphere around a set](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image004.png)
4. Select Style > Side Chains > Stick to better view these residues
![Screenshot from the iCn3D website, Style > Side Chains > Stick](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image006.png)
5. Click Select > Save Selection and name resi_3.5_dna
![Screenshot from the iCn3D website, Select > Save Selection](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image008.png)
6. In Defined Sets, Select nucleotides +Ctrl resi_5a_zn and View > View Selection to view DNA and the interacting residues![Screenshot from the iCn3D website, View > View Selection](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image010.png)
7. View residue Lys120
Note: A handful of residues interacting with the DNA. Lys120 is of particular interest because it’s pointing into the major groove and it’s a positively charged residue.![Screenshot from the iCn3D website, Residues interacting with the DNA major groove](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image012.png)
8. Click Analysis > Mutation to perform mutation analysis on Lys120
![Screenshot from the iCn3D website, Show the mutations in 3D](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image014.png)
9. Type A to alternate between K120 and A120
![Screenshot from the iCn3D website, Interactions in Wild Type of 1TUP](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image016.png)
![Screenshot from the iCn3D website, Interactions in mutated of 1TUP2](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image018.png)
10. Review Key
![Screenshot from the iCn3D website, Key of interactions](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image020.png)
11. Review interaction maps
![Screenshot from the iCn3D website, Interactions map](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image021.png)
12. Review different interaction maps
![Screenshot from the iCn3D website, Different nteractions map](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image023.png)
13. View Defined Sets by Analysis > Defined Sets to take a closer look at specific interactions
![Screenshot from the iCn3D website, 1TUP and Defined Sets](/ncbi/workshops/2022-10_3d-molecular-structures/images/mutation/image025.png)
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Last Reviewed: October 18, 2022