Manganese in PDB 8vj8: X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod

All present enzymatic activity of X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod:
1.15.1.1;

The structure of X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod, PDB code: 8vj8 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)	38.95 / 1.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.909, 77.909, 235.138, 90, 90, 120
R / Rfree (%)	19.1 / 22.4

The structure of X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Manganese atom in the X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod (pdb code 8vj8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod, PDB code: 8vj8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:11.7 occ:1.00 OD2 A:ASP159 2.0 11.5 1.0 NE2 A:HIS74 2.2 9.2 1.0 O A:HOH407 2.2 13.2 1.0 NE2 A:HIS26 2.2 10.3 1.0 NE2 A:HIS163 2.2 11.2 1.0 CG A:ASP159 3.1 8.6 1.0 CE1 A:HIS74 3.1 12.3 1.0 CE1 A:HIS26 3.1 11.4 1.0 CD2 A:HIS163 3.2 11.4 1.0 CD2 A:HIS74 3.2 13.4 1.0 CD2 A:HIS26 3.2 10.4 1.0 CE1 A:HIS163 3.2 11.3 1.0 OD1 A:ASP159 3.6 9.4 1.0 OH A:TYR34 4.0 21.1 1.0 ND1 A:HIS74 4.2 9.1 1.0 ND1 A:HIS26 4.3 10.8 1.0 ND1 A:HIS163 4.3 12.6 1.0 CG A:HIS74 4.3 8.0 1.0 CG A:HIS26 4.3 8.0 1.0 CG A:HIS163 4.3 12.3 1.0 CB A:ASP159 4.3 10.3 1.0 CZ2 A:TRP123 4.4 8.7 1.0 CB A:PHE161 4.5 11.1 1.0 NE2 A:GLN143 4.6 13.1 1.0 CG A:PHE161 4.7 10.4 1.0 CE2 A:TYR34 4.8 18.5 1.0 CZ A:TYR34 4.9 15.5 1.0 CD1 A:PHE161 5.0 10.5 1.0

Manganese binding site 2 out of 2 in the X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Counterpart to Neutron Structure of Reduced TRP161PHE Mnsod within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:10.2 occ:1.00 OD2 B:ASP159 2.0 8.6 1.0 NE2 B:HIS74 2.2 9.3 1.0 NE2 B:HIS163 2.2 8.7 1.0 NE2 B:HIS26 2.2 10.5 1.0 O B:HOH432 2.2 14.7 1.0 CG B:ASP159 3.1 11.1 1.0 CE1 B:HIS74 3.1 8.9 1.0 CD2 B:HIS163 3.1 9.7 1.0 CE1 B:HIS26 3.2 7.9 1.0 CD2 B:HIS26 3.2 7.1 1.0 CE1 B:HIS163 3.2 11.9 1.0 CD2 B:HIS74 3.2 8.2 1.0 OD1 B:ASP159 3.5 7.0 1.0 OH B:TYR34 3.9 13.6 1.0 ND1 B:HIS74 4.2 6.5 1.0 ND1 B:HIS26 4.3 7.7 1.0 ND1 B:HIS163 4.3 8.5 1.0 CG B:HIS163 4.3 7.7 1.0 CG B:HIS74 4.3 5.9 1.0 CG B:HIS26 4.3 8.2 1.0 CB B:ASP159 4.4 9.5 1.0 CZ2 B:TRP123 4.4 8.1 1.0 CB B:PHE161 4.4 9.8 1.0 NE2 B:GLN143 4.6 12.1 1.0 CG B:PHE161 4.7 9.3 1.0 CE2 B:TYR34 4.8 13.0 1.0 CZ B:TYR34 4.9 14.0 1.0 CD1 B:PHE161 4.9 12.4 1.0 CB B:ALA164 5.0 9.8 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