Manganese in PDB 5gxo: Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase

All present enzymatic activity of Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase:
1.15.1.1;

The structure of Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase, PDB code: 5gxo was solved by J.Lu, J.Li, M.Wu, J.Wang, Q.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.74 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.120, 80.120, 242.870, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 25

The binding sites of Manganese atom in the Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase (pdb code 5gxo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase, PDB code: 5gxo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:27.4 occ:1.00 OD2 A:ASP183 2.0 19.2 1.0 NE2 A:HIS98 2.2 23.6 1.0 NE2 A:HIS50 2.2 21.8 1.0 O A:HOH424 2.3 22.9 1.0 NE2 A:HIS187 2.3 22.4 1.0 CG A:ASP183 3.1 21.2 1.0 CE1 A:HIS98 3.2 22.2 1.0 CD2 A:HIS50 3.2 19.8 1.0 CE1 A:HIS50 3.2 21.4 1.0 CD2 A:HIS187 3.2 22.7 1.0 CD2 A:HIS98 3.2 22.8 1.0 CE1 A:HIS187 3.3 22.0 1.0 OD1 A:ASP183 3.5 19.6 1.0 ND1 A:HIS98 4.3 22.3 1.0 ND1 A:HIS50 4.3 22.3 1.0 CG A:HIS50 4.3 21.7 1.0 CG A:HIS98 4.4 23.2 1.0 ND1 A:HIS187 4.4 23.4 1.0 CG A:HIS187 4.4 22.2 1.0 CZ2 A:TRP147 4.4 21.8 1.0 CB A:ASP183 4.4 19.7 1.0 NE2 A:GLN167 4.5 22.4 1.0 CB A:TRP185 4.6 17.1 1.0 CG A:TRP185 4.7 17.8 1.0 CH2 A:TRP147 4.9 22.1 1.0 CD1 A:TRP185 4.9 17.0 1.0

Manganese binding site 2 out of 2 in the Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Discovery of A Compound That Activates SIRT3 to Deacetylate Manganese Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:30.1 occ:1.00 OD2 B:ASP183 2.1 23.5 1.0 NE2 B:HIS50 2.2 25.1 1.0 NE2 B:HIS98 2.2 22.8 1.0 NE2 B:HIS187 2.2 28.3 1.0 O B:HOH428 2.2 28.4 1.0 CE1 B:HIS50 3.1 23.7 1.0 CG B:ASP183 3.1 22.0 1.0 CE1 B:HIS187 3.1 26.9 1.0 CE1 B:HIS98 3.2 23.2 1.0 CD2 B:HIS50 3.2 22.0 1.0 CD2 B:HIS98 3.2 21.9 1.0 CD2 B:HIS187 3.2 26.8 1.0 OD1 B:ASP183 3.4 20.0 1.0 ND1 B:HIS50 4.2 24.4 1.0 ND1 B:HIS187 4.3 25.4 1.0 ND1 B:HIS98 4.3 23.6 1.0 CZ2 B:TRP147 4.3 22.1 1.0 CG B:HIS50 4.3 23.2 1.0 CG B:HIS187 4.3 25.0 1.0 CG B:HIS98 4.4 21.9 1.0 CB B:ASP183 4.4 23.4 1.0 CB B:TRP185 4.5 24.5 1.0 NE2 B:GLN167 4.5 25.9 1.0 CG B:TRP185 4.6 22.8 1.0 CD1 B:TRP185 4.8 22.9 1.0 CB B:ALA188 4.8 28.1 1.0 CH2 B:TRP147 4.9 20.0 1.0

J.Lu, H.Zhang, X.Chen, Y.Zou, J.Li, L.Wang, M.Wu, J.Zang, Y.Yu, W.Zhuang, Q.Xia, J.Wang. A Small Molecule Activator of SIRT3 Promotes Deacetylation and Activation of Manganese Superoxide Dismutase. Free Radic. Biol. Med. V. 112 287 2017.
ISSN: ISSN 1873-4596
PubMed: 28711502
DOI: 10.1016/J.FREERADBIOMED.2017.07.012