Manganese in PDB 2cdy: Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans

All present enzymatic activity of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans:
1.15.1.1;

The structure of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans, PDB code: 2cdy was solved by R.Dennis, E.Micossi, J.Mccarthy, E.Moe, E.Gordon, G.Leonard, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.577, 87.100, 116.418, 90.00, 92.10, 90.00
R / Rfree (%)	17.3 / 22.1

The binding sites of Manganese atom in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans (pdb code 2cdy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans, PDB code: 2cdy:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1211 b:10.9 occ:1.00 OD2 A:ASP172 1.9 8.5 1.0 NE2 A:HIS80 2.1 11.9 1.0 NE2 A:HIS26 2.2 8.9 1.0 NE2 A:HIS176 2.2 10.2 1.0 O A:HOH2183 2.3 6.8 1.0 CG A:ASP172 3.0 9.6 1.0 CE1 A:HIS80 3.1 13.6 1.0 CD2 A:HIS80 3.2 12.8 1.0 CD2 A:HIS26 3.2 8.7 1.0 CD2 A:HIS176 3.2 11.2 1.0 CE1 A:HIS26 3.2 10.7 1.0 CE1 A:HIS176 3.2 12.5 1.0 OD1 A:ASP172 3.5 10.7 1.0 ND1 A:HIS80 4.2 12.9 1.0 CB A:ASP172 4.3 10.6 1.0 CG A:HIS80 4.3 10.1 1.0 ND1 A:HIS26 4.3 8.1 1.0 ND1 A:HIS176 4.3 11.2 1.0 CG A:HIS26 4.3 9.2 1.0 CG A:HIS176 4.4 9.6 1.0 CZ2 A:TRP133 4.4 9.2 1.0 CB A:TRP174 4.6 10.3 1.0 NE2 A:GLN151 4.6 10.3 1.0 CG A:TRP174 4.8 10.9 1.0 CB A:ALA177 4.9 8.8 1.0 CH2 A:TRP133 5.0 9.4 1.0

Manganese binding site 2 out of 4 in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1211 b:17.3 occ:1.00 OD2 B:ASP172 1.9 17.0 1.0 NE2 B:HIS80 2.1 25.5 1.0 NE2 B:HIS26 2.2 15.2 1.0 O B:HOH2100 2.2 15.6 1.0 NE2 B:HIS176 2.3 15.9 1.0 CG B:ASP172 3.0 16.5 1.0 CE1 B:HIS80 3.1 24.4 1.0 CE1 B:HIS26 3.1 15.3 1.0 CD2 B:HIS80 3.1 23.6 1.0 CD2 B:HIS26 3.2 15.4 1.0 CD2 B:HIS176 3.2 15.1 1.0 CE1 B:HIS176 3.3 14.9 1.0 OD1 B:ASP172 3.5 15.8 1.0 ND1 B:HIS80 4.2 21.4 1.0 ND1 B:HIS26 4.2 14.5 1.0 CG B:HIS80 4.2 22.9 1.0 CB B:ASP172 4.2 16.4 1.0 CG B:HIS26 4.3 16.3 1.0 CG B:HIS176 4.4 13.6 1.0 ND1 B:HIS176 4.4 13.9 1.0 CZ2 B:TRP133 4.5 14.0 1.0 NE2 B:GLN151 4.5 14.0 1.0 CB B:TRP174 4.6 12.2 1.0 CG B:TRP174 4.8 12.4 1.0 CB B:ALA177 5.0 14.0 1.0

Manganese binding site 3 out of 4 in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1211 b:13.0 occ:1.00 OD2 C:ASP172 1.9 12.4 1.0 NE2 C:HIS80 2.1 17.3 1.0 O C:HOH2120 2.2 10.4 1.0 NE2 C:HIS176 2.2 10.9 1.0 NE2 C:HIS26 2.2 13.4 1.0 CG C:ASP172 3.0 14.6 1.0 CE1 C:HIS80 3.1 17.9 1.0 CD2 C:HIS80 3.1 17.0 1.0 CD2 C:HIS176 3.2 13.6 1.0 CE1 C:HIS26 3.2 14.9 1.0 CD2 C:HIS26 3.2 15.3 1.0 CE1 C:HIS176 3.2 13.8 1.0 OD1 C:ASP172 3.4 16.1 1.0 ND1 C:HIS80 4.2 16.4 1.0 CG C:HIS80 4.3 16.9 1.0 ND1 C:HIS26 4.3 13.4 1.0 CB C:ASP172 4.3 14.1 1.0 ND1 C:HIS176 4.3 12.7 1.0 CG C:HIS176 4.3 13.2 1.0 CG C:HIS26 4.3 15.8 1.0 CZ2 C:TRP133 4.4 13.6 1.0 NE2 C:GLN151 4.6 12.2 1.0 CB C:TRP174 4.6 13.7 1.0 CG C:TRP174 4.7 13.3 1.0 CB C:ALA177 4.9 14.9 1.0 CD1 C:TRP174 4.9 13.6 1.0 CH2 C:TRP133 5.0 13.4 1.0

Manganese binding site 4 out of 4 in the Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Manganese Superoxide Dismutase (Mn-Sod) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1211 b:15.7 occ:1.00 OD2 D:ASP172 2.0 11.9 1.0 NE2 D:HIS80 2.1 17.2 1.0 NE2 D:HIS26 2.2 15.3 1.0 O D:HOH2164 2.2 11.1 1.0 NE2 D:HIS176 2.3 11.6 1.0 CG D:ASP172 3.0 12.6 1.0 CE1 D:HIS80 3.1 17.1 1.0 CD2 D:HIS80 3.1 15.8 1.0 CD2 D:HIS26 3.2 15.2 1.0 CE1 D:HIS26 3.2 15.1 1.0 CD2 D:HIS176 3.2 12.2 1.0 CE1 D:HIS176 3.3 14.1 1.0 OD1 D:ASP172 3.5 13.0 1.0 ND1 D:HIS80 4.2 16.0 1.0 CG D:HIS80 4.2 15.4 1.0 CB D:ASP172 4.3 11.9 1.0 ND1 D:HIS26 4.3 13.2 1.0 CG D:HIS26 4.3 16.1 1.0 CZ2 D:TRP133 4.4 12.2 1.0 ND1 D:HIS176 4.4 11.6 1.0 CG D:HIS176 4.4 12.1 1.0 NE2 D:GLN151 4.6 12.2 1.0 CB D:TRP174 4.7 11.8 1.0 CG D:TRP174 4.8 11.4 1.0 CB D:ALA177 4.9 12.6 1.0 CH2 D:TRP133 5.0 12.2 1.0

R.J.Dennis, E.Micossi, J.Mccarthy, E.Moe, E.J.Gordon, S.Kozielski-Stuhrmann, G.A.Leonard, S.Mcsweeney. Structure of the Manganese Superoxide Dismutase From Deinococcus Radiodurans in Two Crystal Forms. Acta Crystallogr. Sect. F V. 62 325 2006STRUCT. Biol. Cryst. Commun..
ISSN: ESSN 1744-3091
PubMed: 16582477
DOI: 10.1107/S1744309106008402