Zinc in PDB 5o40: SOD1 Bound to Ebselen

All present enzymatic activity of SOD1 Bound to Ebselen:
1.15.1.1;

The structure of SOD1 Bound to Ebselen, PDB code: 5o40 was solved by M.J.Capper, G.S.A.Wright, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.100, 67.840, 51.040, 90.00, 106.35, 90.00
R / Rfree (%)	16.8 / 21.5

The binding sites of Zinc atom in the SOD1 Bound to Ebselen (pdb code 5o40). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the SOD1 Bound to Ebselen, PDB code: 5o40:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the SOD1 Bound to Ebselen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SOD1 Bound to Ebselen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:8.1 occ:1.00 OD1 A:ASP83 2.0 6.9 1.0 ND1 A:HIS80 2.0 6.7 1.0 ND1 A:HIS63 2.1 8.9 1.0 ND1 A:HIS71 2.1 8.1 1.0 CG A:ASP83 2.7 6.7 1.0 OD2 A:ASP83 2.8 6.7 1.0 CE1 A:HIS80 2.9 6.2 1.0 CE1 A:HIS71 2.9 8.6 1.0 CE1 A:HIS63 3.0 8.4 1.0 CG A:HIS80 3.1 5.9 1.0 CG A:HIS63 3.1 9.1 1.0 CG A:HIS71 3.1 8.2 1.0 CB A:HIS63 3.5 8.5 1.0 CB A:HIS80 3.5 5.8 1.0 CB A:HIS71 3.6 9.7 1.0 CA A:HIS71 3.9 9.0 1.0 NE2 A:HIS80 4.0 6.7 1.0 NE2 A:HIS71 4.1 8.1 1.0 CD2 A:HIS80 4.1 6.0 1.0 NE2 A:HIS63 4.1 9.0 1.0 O A:LYS136 4.1 13.8 1.0 CB A:ASP83 4.1 6.1 1.0 CD2 A:HIS63 4.2 10.1 1.0 CD2 A:HIS71 4.2 8.8 1.0 N A:HIS80 4.6 6.2 1.0 N A:GLY72 4.6 9.1 1.0 CA A:HIS80 4.7 5.9 1.0 CA A:ASP83 4.7 5.5 1.0 C A:HIS71 4.8 8.3 1.0 N A:HIS71 4.9 8.9 1.0 N A:ASP83 4.9 5.7 1.0 CA A:HIS63 5.0 7.7 1.0

Zinc binding site 2 out of 4 in the SOD1 Bound to Ebselen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SOD1 Bound to Ebselen within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:7.4 occ:0.80 NE2 A:HIS120 2.0 7.7 1.0 O4 A:SO4504 2.0 7.4 0.8 NE2 A:HIS48 2.1 8.4 1.0 ND1 A:HIS46 2.1 7.9 1.0 CE1 A:HIS120 2.9 8.6 1.0 CE1 A:HIS48 2.9 8.5 1.0 CD2 A:HIS120 3.0 7.0 1.0 CE1 A:HIS46 3.0 8.6 1.0 CG A:HIS46 3.1 7.2 1.0 CD2 A:HIS48 3.2 7.9 1.0 S A:SO4504 3.2 8.3 0.8 O2 A:SO4504 3.4 8.4 0.8 CB A:HIS46 3.5 5.6 1.0 NE2 A:HIS63 3.6 9.0 1.0 ND1 A:HIS120 4.0 8.1 1.0 CD2 A:HIS63 4.0 10.1 1.0 CG A:HIS120 4.1 7.1 1.0 O1 A:SO4504 4.1 9.3 0.8 ND1 A:HIS48 4.1 7.6 1.0 NE2 A:HIS46 4.2 7.4 1.0 O3 A:SO4504 4.2 10.1 0.8 CD2 A:HIS46 4.2 6.8 1.0 CG A:HIS48 4.3 7.0 1.0 O A:HOH629 4.5 11.9 1.0 CE1 A:HIS63 4.5 8.4 1.0 CG1 A:VAL118 4.5 5.8 1.0 CB A:VAL118 4.6 6.7 1.0 NE A:ARG143 4.9 9.8 1.0 CA A:HIS46 4.9 5.2 1.0

Zinc binding site 3 out of 4 in the SOD1 Bound to Ebselen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SOD1 Bound to Ebselen within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:8.2 occ:1.00 OD1 F:ASP83 2.0 7.3 1.0 ND1 F:HIS80 2.0 6.9 1.0 ND1 F:HIS63 2.0 8.7 1.0 ND1 F:HIS71 2.1 8.8 1.0 CG F:ASP83 2.7 6.5 1.0 OD2 F:ASP83 2.8 6.5 1.0 CE1 F:HIS80 2.9 6.7 1.0 CE1 F:HIS71 3.0 9.2 1.0 CE1 F:HIS63 3.0 8.2 1.0 CG F:HIS80 3.1 6.8 1.0 CG F:HIS63 3.1 9.2 1.0 CG F:HIS71 3.2 8.7 1.0 CB F:HIS63 3.4 7.3 1.0 CB F:HIS80 3.5 6.3 1.0 CB F:HIS71 3.6 10.4 1.0 CA F:HIS71 3.9 10.0 1.0 O F:LYS136 4.0 12.8 1.0 NE2 F:HIS80 4.0 7.5 1.0 NE2 F:HIS63 4.1 10.1 1.0 CD2 F:HIS80 4.1 6.4 1.0 NE2 F:HIS71 4.1 8.4 1.0 CB F:ASP83 4.2 5.6 1.0 CD2 F:HIS63 4.2 9.8 1.0 CD2 F:HIS71 4.3 9.7 1.0 N F:HIS80 4.6 6.0 1.0 CA F:HIS80 4.7 6.0 1.0 N F:GLY72 4.7 9.7 1.0 CA F:ASP83 4.7 5.7 1.0 O F:HOH692 4.8 42.5 1.0 N F:HIS71 4.8 8.6 1.0 C F:HIS71 4.9 9.1 1.0 N F:ASP83 4.9 6.4 1.0 CA F:HIS63 5.0 6.8 1.0 C F:LYS136 5.0 12.4 1.0

Zinc binding site 4 out of 4 in the SOD1 Bound to Ebselen


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SOD1 Bound to Ebselen within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:8.2 occ:0.80 O1 F:SO4504 2.0 9.3 0.8 NE2 F:HIS120 2.0 10.9 1.0 ND1 F:HIS46 2.1 8.7 1.0 NE2 F:HIS48 2.1 8.4 1.0 CE1 F:HIS120 2.9 10.7 1.0 CD2 F:HIS120 3.0 9.6 1.0 CE1 F:HIS48 3.0 8.9 1.0 CE1 F:HIS46 3.0 11.6 1.0 CG F:HIS46 3.1 7.1 1.0 S F:SO4504 3.1 9.7 0.8 CD2 F:HIS48 3.2 7.9 1.0 O4 F:SO4504 3.4 9.7 0.8 CB F:HIS46 3.5 5.5 1.0 NE2 F:HIS63 3.6 10.1 1.0 CD2 F:HIS63 4.0 9.8 1.0 ND1 F:HIS120 4.0 9.8 1.0 CG F:HIS120 4.1 8.0 1.0 O3 F:SO4504 4.1 11.0 0.8 O2 F:SO4504 4.1 10.6 0.8 ND1 F:HIS48 4.1 8.2 1.0 NE2 F:HIS46 4.2 8.8 1.0 CD2 F:HIS46 4.2 7.5 1.0 CG F:HIS48 4.3 7.7 1.0 O F:HOH618 4.4 11.8 1.0 CG1 F:VAL118 4.4 7.2 1.0 CE1 F:HIS63 4.5 8.2 1.0 CB F:VAL118 4.6 6.8 1.0 NE F:ARG143 4.9 12.0 1.0 CA F:HIS46 4.9 5.5 1.0

M.J.Capper, G.S.A.Wright, L.Barbieri, E.Luchinat, E.Mercatelli, L.Mcalary, J.J.Yerbury, P.M.O'neill, S.V.Antonyuk, L.Banci, S.S.Hasnain. The Cysteine-Reactive Small Molecule Ebselen Facilitates Effective SOD1 Maturation. Nat Commun V. 9 1693 2018.
ISSN: ESSN 2041-1723
PubMed: 29703933
DOI: 10.1038/S41467-018-04114-X