Manganese in PDB 5vf9: Native Human Manganese Superoxide Dismutase

All present enzymatic activity of Native Human Manganese Superoxide Dismutase:
1.15.1.1;

The structure of Native Human Manganese Superoxide Dismutase, PDB code: 5vf9 was solved by J.Azadmanesh, S.R.Trickel, G.E.O.Borgstahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.50 / 1.82
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.240, 78.240, 238.470, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.1

The structure of Native Human Manganese Superoxide Dismutase also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Manganese atom in the Native Human Manganese Superoxide Dismutase (pdb code 5vf9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Native Human Manganese Superoxide Dismutase, PDB code: 5vf9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Native Human 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 Native Human Manganese Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:16.0 occ:1.00 OD2 A:ASP159 2.0 14.8 1.0 O A:HOH301 2.2 15.3 1.0 NE2 A:HIS74 2.2 14.7 1.0 NE2 A:HIS163 2.3 15.7 1.0 NE2 A:HIS26 2.3 15.1 1.0 CG A:ASP159 3.1 14.7 1.0 CD2 A:HIS163 3.1 14.8 1.0 CE1 A:HIS74 3.2 15.4 1.0 CD2 A:HIS26 3.2 14.6 1.0 CE1 A:HIS26 3.2 14.5 1.0 CD2 A:HIS74 3.3 15.0 1.0 CE1 A:HIS163 3.3 14.9 1.0 OD1 A:ASP159 3.5 14.5 1.0 CZ2 A:TRP123 4.3 13.9 1.0 ND1 A:HIS74 4.3 15.5 1.0 CG A:HIS163 4.3 15.4 1.0 ND1 A:HIS26 4.3 14.7 1.0 CG A:HIS26 4.3 14.9 1.0 CB A:ASP159 4.4 14.0 1.0 ND1 A:HIS163 4.4 15.3 1.0 CG A:HIS74 4.4 15.2 1.0 NE2 A:GLN143 4.5 18.4 1.0 CB A:TRP161 4.5 14.4 1.0 CG A:TRP161 4.7 14.5 1.0 CH2 A:TRP123 4.9 13.6 1.0 CD1 A:TRP161 4.9 14.2 1.0 CB A:ALA164 5.0 15.7 1.0

Manganese binding site 2 out of 2 in the Native Human 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 Native Human Manganese Superoxide Dismutase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:17.6 occ:1.00 OD2 B:ASP159 2.0 16.3 1.0 O B:HOH301 2.2 15.9 1.0 NE2 B:HIS26 2.2 15.4 1.0 NE2 B:HIS163 2.2 17.3 1.0 NE2 B:HIS74 2.3 17.1 1.0 CG B:ASP159 3.1 15.7 1.0 CD2 B:HIS163 3.1 16.5 1.0 CD2 B:HIS26 3.2 14.5 1.0 CD2 B:HIS74 3.2 16.1 1.0 CE1 B:HIS26 3.2 14.9 1.0 CE1 B:HIS74 3.2 15.8 1.0 CE1 B:HIS163 3.3 16.8 1.0 OD1 B:ASP159 3.5 14.9 1.0 ND1 B:HIS26 4.3 14.9 1.0 CG B:HIS26 4.3 14.6 1.0 CG B:HIS163 4.3 16.4 1.0 CZ2 B:TRP123 4.3 14.0 1.0 ND1 B:HIS74 4.3 15.0 1.0 ND1 B:HIS163 4.3 16.5 1.0 CG B:HIS74 4.4 15.3 1.0 CB B:ASP159 4.4 15.2 1.0 CB B:TRP161 4.4 14.7 1.0 NE2 B:GLN143 4.5 17.4 1.0 CG B:TRP161 4.6 14.9 1.0 CD1 B:TRP161 4.9 15.6 1.0 CH2 B:TRP123 4.9 14.5 1.0 CB B:ALA164 5.0 16.1 1.0

J.Azadmanesh, S.R.Trickel, G.E.O.Borgstahl. Substrate-Analog Binding and Electrostatic Surfaces of Human Manganese Superoxide Dismutase. J. Struct. Biol. V. 199 68 2017.
ISSN: ESSN 1095-8657
PubMed: 28461152
DOI: 10.1016/J.JSB.2017.04.011