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


3. Choose nucleotides, set sphere radius to 3.5 Å, choose 1TUP_B, and click on Display

4. Select Style > Side Chains > Stick to better view these residues


5. Click Select > Save Selection and name resi_3.5_dna


6. In Defined Sets, Select nucleotides +Ctrl resi_5a_zn and View > View Selection to view DNA and the interacting residues

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.

8. Click Analysis > Mutation to perform mutation analysis on Lys120


9. Type A to alternate between K120 and A120

10. Review Key


11. Review interaction maps

12. Review different interaction maps


13. View Defined Sets by Analysis > Defined Sets to take a closer look at specific interactions

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