Crystal structure of ni-containing superoxide dismutase with ni-ligation corresponding to the state after full X- ray-induced reduction

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).

Ligands and binding sites

• NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, F, E
• SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E, F, D
• ACY · Acetic acid · additive · 3 copies · chains C, D, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

12 interfaces between chains.

• D–F · 997 Ų buried · 14 hydrogen bonds · protein-protein
• B–E · 942 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 933 Ų buried · 14 hydrogen bonds · protein-protein
• A–F · 864 Ų buried · 18 hydrogen bonds · protein-protein
• D–E · 861 Ų buried · 19 hydrogen bonds · protein-protein

Compared structures

• 1Q0M · Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to… · the same entry in another collection · chain C against C, TM-score 1.00
• P80734 · AlphaFold monomer V2.0 prediction for superoxide dismutase [ni] (P80734) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P80734
• Elsewhere: RCSB PDB 1Q0M · PDBe 1Q0M · UniProt P80734