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iCn3D Skill: Displays surface of a protein - Superoxide Dismutase

Last updated

Jan 9, 2025
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A. The molecular surface of superoxide dismutase

PDB ID: 2sod

Description
superoxide dismutase
dimer with 2 Cu²⁺ ions bound in each subunit
catalyses the reaction of O₂^- + O₂^- + 2H⁺ → H₂O₂ + O₂

Instructions

File, Retrieve by ID, MMDB
Style, Surface Opacity, Fast Transparency, 0.2
Select, Select on 3D, Chain. Alt Click on one chain
Color, Secondary, Sheets in Yellow
Style, Surface Type, Molecular (takes a while to render)
Now Alt Click on the other chain
Color, Wimley White Hydrophobicity* (takes a while to render)
Style, Surface Type, Molecular (takes a while to render)
Style, Background, White
File, Share Link, Save short url

B. The electrostatic surface potential of superoxide dismutase

Background: Superoxide (O₂^-) is a toxic free radical and hence dangerous. To capture it as effectively as possible, the surface distribution of charged side changes is such that a positve electrostatic potential surrounds each active site.

File, Retrieve by ID, MMDB
Select, Select on 3D, Chain. Alt Click on one chain, Control-click on the second. Alternatively, choose Analysis, Sequence and Annotations, Details Tabs (uncheck conserved domains), and click one chain (blue font) and then control-click the second so both are highlighted.
In the Details tab of Analysis, Sequence and Annotations, sweep both Cu ions (with mouse) to select them, the Color, Yellow
Analysis, DelPhi Potential, DelPhi Potential
Choose the Surface with Potential Map tab. Chose the options below
Select Surface with Potential. Look a the blue (positive potential) surround the yellow Zn ions in both active sites.
Style, Surface Type, Molecular (takes a while to render)
Style, Background, White
File, Share Link, Save short url

A. The molecular surface of superoxide dismutase

B. The electrostatic surface potential of superoxide dismutase

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