Zinc in PDB 5o3y: SOD1 Bound to Ebsulfur

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

The structure of SOD1 Bound to Ebsulfur, PDB code: 5o3y 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)	49.01 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.050, 67.960, 51.180, 90.00, 106.73, 90.00
R / Rfree (%)	15.1 / 18.6

The binding sites of Zinc atom in the SOD1 Bound to Ebsulfur (pdb code 5o3y). 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 Ebsulfur, PDB code: 5o3y:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 Ebsulfur within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:9.4 occ:1.00 OD1 A:ASP83 2.0 8.5 1.0 ND1 A:HIS63 2.0 10.7 1.0 ND1 A:HIS80 2.0 9.1 1.0 ND1 A:HIS71 2.1 9.5 1.0 CG A:ASP83 2.7 8.0 1.0 OD2 A:ASP83 2.8 8.7 1.0 CE1 A:HIS80 2.9 9.0 1.0 CE1 A:HIS71 2.9 10.8 1.0 CE1 A:HIS63 2.9 12.5 1.0 CG A:HIS63 3.1 13.4 1.0 CG A:HIS80 3.1 8.6 1.0 CG A:HIS71 3.2 9.5 1.0 CB A:HIS63 3.5 11.0 1.0 CB A:HIS80 3.5 8.3 1.0 CB A:HIS71 3.6 10.7 1.0 CA A:HIS71 3.9 10.7 1.0 O A:LYS136 4.0 16.6 1.0 NE2 A:HIS80 4.0 9.8 1.0 NE2 A:HIS63 4.1 14.9 1.0 NE2 A:HIS71 4.1 9.9 1.0 CD2 A:HIS80 4.1 8.7 1.0 CB A:ASP83 4.1 7.7 1.0 CD2 A:HIS63 4.2 16.8 1.0 CD2 A:HIS71 4.2 10.8 1.0 O A:HOH663 4.4 32.1 1.0 N A:HIS80 4.6 7.6 1.0 N A:GLY72 4.7 10.8 1.0 CA A:ASP83 4.7 7.3 1.0 CA A:HIS80 4.7 8.0 1.0 C A:HIS71 4.8 10.0 1.0 N A:HIS71 4.9 10.0 1.0 N A:ASP83 4.9 7.2 1.0 CA A:HIS63 5.0 10.6 1.0

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


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 Ebsulfur within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:9.1 occ:0.60 NE2 A:HIS120 2.0 11.3 1.0 O4 A:SO4504 2.0 11.0 0.7 NE2 A:HIS48 2.1 11.4 1.0 ND1 A:HIS46 2.2 12.1 1.0 CE1 A:HIS120 2.8 12.4 1.0 CE1 A:HIS48 2.8 12.8 1.0 CD2 A:HIS120 3.0 9.7 1.0 CE1 A:HIS46 3.1 14.3 1.0 S A:SO4504 3.2 13.8 0.7 CD2 A:HIS48 3.2 10.3 1.0 CG A:HIS46 3.2 11.0 1.0 NE2 A:HIS63 3.4 14.9 1.0 O2 A:SO4504 3.5 14.2 0.7 CB A:HIS46 3.6 8.8 1.0 CD2 A:HIS63 3.8 16.8 1.0 ND1 A:HIS120 3.9 11.2 1.0 O1 A:SO4504 4.0 19.6 0.7 CG A:HIS120 4.0 9.6 1.0 ND1 A:HIS48 4.0 10.6 1.0 O3 A:SO4504 4.2 18.1 0.7 NE2 A:HIS46 4.2 12.9 1.0 CG A:HIS48 4.3 9.0 1.0 CD2 A:HIS46 4.3 10.3 1.0 CE1 A:HIS63 4.4 12.5 1.0 O A:HOH609 4.5 19.9 1.0 CG1 A:VAL118 4.6 9.6 1.0 CB A:VAL118 4.7 7.7 1.0 NE A:ARG143 4.8 11.7 1.0 CG A:HIS63 4.9 13.4 1.0 CA A:HIS46 5.0 7.9 1.0

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


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 Ebsulfur within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:10.3 occ:1.00 OD1 F:ASP83 2.0 9.9 1.0 ND1 F:HIS80 2.0 9.8 1.0 ND1 F:HIS71 2.1 9.7 1.0 ND1 F:HIS63 2.1 11.7 1.0 CG F:ASP83 2.7 9.8 1.0 OD2 F:ASP83 2.8 10.2 1.0 CE1 F:HIS80 2.9 8.7 1.0 CE1 F:HIS71 2.9 11.0 1.0 CE1 F:HIS63 3.0 13.6 1.0 CG F:HIS80 3.1 9.4 1.0 CG F:HIS63 3.1 12.4 1.0 CG F:HIS71 3.2 10.5 1.0 CB F:HIS63 3.4 10.9 1.0 CB F:HIS80 3.5 8.7 1.0 CB F:HIS71 3.6 11.9 1.0 CA F:HIS71 3.9 11.4 1.0 O F:LYS136 3.9 16.2 1.0 NE2 F:HIS80 4.0 10.0 1.0 NE2 F:HIS71 4.1 10.9 1.0 NE2 F:HIS63 4.1 16.2 1.0 CD2 F:HIS80 4.1 9.0 1.0 CB F:ASP83 4.2 9.3 1.0 CD2 F:HIS63 4.2 14.2 1.0 CD2 F:HIS71 4.2 12.2 1.0 O F:HOH669 4.5 29.6 1.0 N F:HIS80 4.7 9.4 1.0 CA F:ASP83 4.7 9.5 1.0 N F:GLY72 4.7 12.2 1.0 CA F:HIS80 4.7 8.6 1.0 C F:HIS71 4.9 10.3 1.0 N F:ASP83 4.9 9.6 1.0 N F:HIS71 4.9 10.5 1.0 C F:LYS136 4.9 14.5 1.0 CA F:HIS63 5.0 9.5 1.0

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


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 Ebsulfur within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn502 b:10.9 occ:0.50 NE2 F:HIS120 1.9 14.7 1.0 O1 F:SO4504 2.0 14.6 0.7 NE2 F:HIS48 2.1 14.2 1.0 ND1 F:HIS46 2.2 14.8 1.0 CE1 F:HIS120 2.8 17.3 1.0 CE1 F:HIS48 2.8 15.5 1.0 CD2 F:HIS120 2.9 13.5 1.0 CE1 F:HIS46 3.1 20.6 1.0 S F:SO4504 3.2 17.7 0.7 CD2 F:HIS48 3.2 12.7 1.0 CG F:HIS46 3.3 13.3 1.0 NE2 F:HIS63 3.4 16.2 1.0 O4 F:SO4504 3.5 20.0 0.7 CB F:HIS46 3.7 11.3 1.0 CD2 F:HIS63 3.8 14.2 1.0 ND1 F:HIS120 3.9 15.7 1.0 CG F:HIS120 3.9 13.9 1.0 ND1 F:HIS48 4.0 13.2 1.0 O3 F:SO4504 4.1 22.8 0.7 O2 F:SO4504 4.2 21.2 0.7 CG F:HIS48 4.3 12.1 1.0 NE2 F:HIS46 4.3 16.6 1.0 CD2 F:HIS46 4.4 15.6 1.0 CE1 F:HIS63 4.4 13.6 1.0 CG1 F:VAL118 4.5 12.1 1.0 O F:HOH617 4.6 26.1 1.0 CB F:VAL118 4.6 9.8 1.0 NE F:ARG143 4.8 12.7 1.0 CG F:HIS63 4.9 12.4 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