Manganese in PDB 8vj5: Peroxide-Soaked Mnsod

All present enzymatic activity of Peroxide-Soaked Mnsod:
1.15.1.1;

The structure of Peroxide-Soaked Mnsod, PDB code: 8vj5 was solved by J.Azadmanesh, K.Slobodnik, L.R.Struble, W.E.Lutz, K.L.Weiss, D.A.A.Myles, T.Kroll, G.E.O.Borgstahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.10 / 1.76
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.348, 78.348, 236.628, 90, 90, 120
R / Rfree (%)	19.8 / 21.8

The binding sites of Manganese atom in the Peroxide-Soaked Mnsod (pdb code 8vj5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Peroxide-Soaked Mnsod, PDB code: 8vj5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Peroxide-Soaked Mnsod


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peroxide-Soaked Mnsod within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:13.8 occ:1.00 OD2 A:ASP159 2.1 14.6 1.0 NE2 A:HIS26 2.2 9.4 1.0 NE2 A:HIS74 2.2 12.9 1.0 O2 A:PEO202 2.2 16.7 0.6 O1 A:PEO202 2.2 11.4 0.6 NE2 A:HIS163 2.2 15.0 1.0 CE1 A:HIS74 3.1 13.5 1.0 CE1 A:HIS26 3.1 9.8 1.0 CG A:ASP159 3.1 10.4 1.0 CD2 A:HIS163 3.2 10.4 1.0 CD2 A:HIS26 3.2 10.4 1.0 CE1 A:HIS163 3.2 15.3 1.0 CD2 A:HIS74 3.2 10.2 1.0 OD1 A:ASP159 3.5 12.0 1.0 ND1 A:HIS26 4.2 12.6 1.0 ND1 A:HIS74 4.2 14.2 1.0 CG A:HIS26 4.3 12.0 1.0 ND1 A:HIS163 4.3 15.7 1.0 CG A:HIS74 4.3 13.8 1.0 CG A:HIS163 4.3 15.6 1.0 CZ2 A:TRP123 4.4 13.8 1.0 CB A:ASP159 4.4 9.7 1.0 NE2 A:GLN143 4.5 17.2 1.0 CB A:TRP161 4.5 12.7 1.0 CG A:TRP161 4.7 15.9 1.0 CH2 A:TRP123 5.0 9.5 1.0 CD1 A:TRP161 5.0 13.2 1.0 CB A:ALA164 5.0 11.7 1.0

Manganese binding site 2 out of 2 in the Peroxide-Soaked Mnsod


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peroxide-Soaked Mnsod within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:15.2 occ:1.00 OD2 B:ASP159 2.1 15.1 1.0 O1 B:PEO202 2.1 13.9 0.5 NE2 B:HIS26 2.2 12.1 1.0 NE2 B:HIS74 2.2 17.1 1.0 NE2 B:HIS163 2.2 14.8 1.0 O2 B:PEO202 2.3 16.5 0.5 CE1 B:HIS26 3.1 17.2 1.0 CE1 B:HIS74 3.1 14.9 1.0 CG B:ASP159 3.1 15.2 1.0 CD2 B:HIS26 3.1 12.0 1.0 CD2 B:HIS74 3.2 15.6 1.0 CD2 B:HIS163 3.2 14.7 1.0 CE1 B:HIS163 3.2 14.8 1.0 OD1 B:ASP159 3.6 13.6 1.0 ND1 B:HIS26 4.2 12.2 1.0 ND1 B:HIS74 4.2 12.6 1.0 CG B:HIS26 4.3 11.1 1.0 CG B:HIS74 4.3 15.3 1.0 CZ2 B:TRP123 4.3 13.6 1.0 ND1 B:HIS163 4.3 13.8 1.0 CG B:HIS163 4.4 13.6 1.0 CB B:ASP159 4.4 11.1 1.0 NE2 B:GLN143 4.5 15.3 1.0 CB B:TRP161 4.5 16.6 1.0 CG B:TRP161 4.7 15.2 1.0 CB B:ALA164 5.0 12.7 1.0 CH2 B:TRP123 5.0 13.2 1.0

J.Azadmanesh, K.Slobodnik, L.R.Struble, W.E.Lutz, L.Coates, K.L.Weiss, D.A.A.Myles, T.Kroll, G.E.O.Borgstahl. Revealing the Atomic and Electronic Mechanism of Human Manganese Superoxide Dismutase Product Inhibition. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 38328249
DOI: 10.1101/2024.01.26.577433