Zinc in PDB 5u9m: Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site

All present enzymatic activity of Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site:
1.15.1.1;

The structure of Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site, PDB code: 5u9m was solved by A.B.Taylor, P.J.Hart, D.D.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.92 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.097, 184.353, 48.514, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.5

The binding sites of Zinc atom in the Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site (pdb code 5u9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site, PDB code: 5u9m:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:28.0 occ:1.00 ND1 A:HIS63 2.0 36.0 1.0 ND1 A:HIS80 2.0 29.5 1.0 OD1 A:ASP83 2.1 28.2 1.0 ND1 A:HIS71 2.1 20.7 1.0 CG A:ASP83 2.7 34.4 1.0 OD2 A:ASP83 2.7 30.3 1.0 CE1 A:HIS80 2.8 31.9 1.0 CE1 A:HIS63 2.9 26.2 1.0 CG A:HIS63 2.9 29.6 1.0 CE1 A:HIS71 3.0 27.2 1.0 CG A:HIS80 3.1 26.7 1.0 CG A:HIS71 3.2 23.2 1.0 CB A:HIS63 3.3 21.9 1.0 CB A:HIS80 3.5 25.5 1.0 CB A:HIS71 3.5 32.7 1.0 CA A:HIS71 3.8 29.2 1.0 O A:LYS136 4.0 36.7 1.0 NE2 A:HIS80 4.0 34.2 1.0 NE2 A:HIS63 4.0 24.7 1.0 CD2 A:HIS63 4.1 24.9 1.0 CD2 A:HIS80 4.1 30.7 1.0 CB A:ASP83 4.2 25.8 1.0 NE2 A:HIS71 4.2 27.5 1.0 CD2 A:HIS71 4.3 25.4 1.0 O A:HOH311 4.5 30.9 1.0 N A:HIS80 4.6 27.3 1.0 N A:GLY72 4.7 28.3 1.0 CA A:HIS80 4.7 30.7 1.0 CA A:ASP83 4.8 31.7 1.0 C A:HIS71 4.8 26.9 1.0 CA A:HIS63 4.8 26.8 1.0 N A:HIS71 4.8 27.8 1.0 C A:LYS136 4.9 34.2 1.0 CA A:THR137 4.9 29.8 1.0 N A:ASP83 5.0 30.2 1.0

Zinc binding site 2 out of 3 in the Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:0.6 occ:0.86 SG B:CYS17 2.3 0.3 1.0 SG B:CYS20 2.4 0.6 1.0 CB B:CYS17 3.2 0.1 1.0 N B:CYS17 3.4 0.9 1.0 CB B:CYS20 3.8 0.3 1.0 CA B:CYS17 3.9 0.6 1.0 N B:CYS20 4.0 0.3 1.0 CA B:CYS20 4.4 0.1 1.0 C B:CYS17 4.5 0.4 1.0 C B:ASN19 4.9 0.1 1.0 CB B:ASN19 4.9 0.6 1.0 O B:CYS17 4.9 0.2 1.0 N B:ASN19 4.9 0.9 1.0

Zinc binding site 3 out of 3 in the Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper-Ion Entry Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.3 occ:1.00 OD1 C:ASP83 1.9 28.9 1.0 ND1 C:HIS80 2.0 30.5 1.0 ND1 C:HIS71 2.1 21.2 1.0 ND1 C:HIS63 2.1 35.3 1.0 CG C:ASP83 2.7 35.8 1.0 OD2 C:ASP83 2.8 29.1 1.0 CE1 C:HIS80 2.8 30.8 1.0 CE1 C:HIS71 3.0 30.6 1.0 CG C:HIS63 3.0 30.7 1.0 CE1 C:HIS63 3.0 25.9 1.0 CG C:HIS71 3.1 22.4 1.0 CG C:HIS80 3.1 24.3 1.0 CB C:HIS63 3.3 24.0 1.0 CB C:HIS71 3.4 30.5 1.0 CB C:HIS80 3.6 27.8 1.0 CA C:HIS71 3.8 33.0 1.0 O C:LYS136 3.8 33.5 1.0 NE2 C:HIS80 4.0 35.3 1.0 NE2 C:HIS63 4.1 21.6 1.0 CB C:ASP83 4.1 25.2 1.0 CD2 C:HIS63 4.1 23.8 1.0 NE2 C:HIS71 4.1 30.3 1.0 CD2 C:HIS80 4.1 31.2 1.0 CD2 C:HIS71 4.2 25.1 1.0 N C:HIS80 4.6 29.0 1.0 O C:HOH314 4.6 24.8 1.0 N C:GLY72 4.6 23.0 1.0 CA C:ASP83 4.7 30.8 1.0 CA C:HIS80 4.7 30.8 1.0 C C:HIS71 4.8 29.8 1.0 C C:LYS136 4.8 36.2 1.0 N C:HIS71 4.8 29.2 1.0 CA C:HIS63 4.9 28.6 1.0 N C:ASP83 4.9 31.6 1.0

M.M.Fetherolf, S.D.Boyd, A.B.Taylor, H.J.Kim, J.A.Wohlschlegel, N.J.Blackburn, P.J.Hart, D.R.Winge, D.D.Winkler. Copper-Zinc Superoxide Dismutase Is Activated Through A Sulfenic Acid Intermediate at A Copper Ion Entry Site. J. Biol. Chem. V. 292 12025 2017.
ISSN: ESSN 1083-351X
PubMed: 28533431
DOI: 10.1074/JBC.M117.775981