Magnesium in PDB 8re2: Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans, PDB code: 8re2 was solved by B.A.Salgueiro, K.Frade, C.Frazao, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.31 / 2.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	64.13, 64.13, 111.322, 90, 90, 120
R / Rfree (%)	18.3 / 23.7

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans (pdb code 8re2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans, PDB code: 8re2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:62.6 occ:1.00 OG1 A:THR30 2.9 53.2 1.0 N A:THR30 3.0 52.8 1.0 OE1 A:GLN28 3.0 50.1 1.0 N A:ALA29 3.3 54.4 1.0 CB A:ALA80 3.4 51.6 1.0 CA A:ALA80 3.4 54.0 1.0 CB A:THR30 3.4 50.6 1.0 CB A:GLN28 3.5 50.0 1.0 O A:THR79 3.5 60.5 1.0 CA A:THR30 3.8 52.7 1.0 C A:GLN28 3.9 55.0 1.0 CD A:GLN28 3.9 49.3 1.0 C A:ALA29 3.9 55.3 1.0 CA A:ALA29 3.9 55.0 1.0 CG A:GLN28 4.0 48.6 1.0 CB A:ALA29 4.0 52.6 1.0 N A:ALA80 4.1 55.9 1.0 C A:THR79 4.1 54.3 1.0 CA A:GLN28 4.1 50.7 1.0 O A:ALA66 4.2 54.7 1.0 CD1 A:TRP78 4.3 56.8 1.0 O A:GLN28 4.7 54.4 1.0 C A:ALA80 4.7 53.5 1.0 CG2 A:ILE65 4.7 52.6 1.0 N A:ALA81 4.8 51.2 1.0 NE1 A:TRP78 4.9 53.2 1.0 CG2 A:THR30 4.9 53.3 1.0 CE A:MET447 4.9 53.5 1.0 SD A:MET447 5.0 58.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:66.5 occ:1.00 OE2 A:GLU366 2.7 64.3 1.0 N A:ASP358 2.8 59.0 1.0 O A:ASP358 2.9 62.4 1.0 CA A:ASP358 3.4 61.9 1.0 NH2 A:ARG371 3.5 53.4 1.0 CB A:ASP358 3.5 63.3 1.0 C A:ASP358 3.5 61.2 1.0 CD1 A:TYR357 3.6 58.0 1.0 CZ A:ARG371 3.6 59.9 1.0 NH1 A:ARG371 3.6 54.3 1.0 CD A:GLU366 3.6 64.9 1.0 CB A:ALA252 3.7 58.5 1.0 C A:TYR357 3.8 61.6 1.0 CE1 A:TYR357 3.9 55.2 1.0 CA A:TYR357 4.0 60.5 1.0 CG A:GLU366 4.1 63.3 1.0 CB A:ALA361 4.2 64.6 1.0 CG A:TYR357 4.2 58.8 1.0 NE A:ARG371 4.3 56.9 1.0 ND2 A:ASN256 4.3 63.0 1.0 O A:ALA361 4.6 67.7 1.0 CB A:TYR357 4.6 56.7 1.0 OE1 A:GLU366 4.6 66.5 1.0 O A:ALA356 4.7 57.6 1.0 CG A:ASP358 4.7 67.2 1.0 CZ A:TYR357 4.8 58.8 1.0 N A:PRO359 4.8 62.0 1.0 O A:TYR357 5.0 59.7 1.0 CA A:ALA252 5.0 55.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) From Deinoccoccus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:67.3 occ:1.00 OE2 A:GLU370 2.6 76.4 1.0 OH A:TYR353 2.7 49.7 1.0 CD A:GLU370 2.9 76.7 1.0 CG A:GLU370 3.2 71.3 1.0 ND1 A:HIS249 3.3 54.1 1.0 CE1 A:TYR353 3.5 56.2 1.0 CZ A:TYR353 3.5 55.3 1.0 O A:ARG371 3.6 54.8 1.0 NH2 A:ARG440 3.7 67.8 1.0 OE1 A:GLU370 3.7 73.6 1.0 CA A:GLU370 3.8 61.8 1.0 CB A:HIS249 3.9 51.3 1.0 N A:ARG371 3.9 59.0 1.0 C A:GLU370 3.9 61.7 1.0 CG A:HIS249 4.0 55.8 1.0 CB A:GLU370 4.1 66.7 1.0 CZ A:ARG440 4.1 69.7 1.0 CA A:HIS249 4.2 51.8 1.0 C A:ARG371 4.2 58.9 1.0 NH1 A:ARG440 4.2 67.1 1.0 CE1 A:HIS249 4.4 56.8 1.0 CE A:LYS247 4.5 58.5 1.0 O A:GLU370 4.6 64.0 1.0 CA A:ARG371 4.6 57.9 1.0 O A:TYR248 4.7 51.9 1.0 CD1 A:TYR353 4.8 54.0 1.0 CE2 A:TYR353 4.8 53.0 1.0 NE A:ARG440 4.9 65.8 1.0 N A:HIS249 5.0 50.3 1.0 NZ A:LYS247 5.0 61.8 1.0

K.Frade, C.M.Silveira, B.A.Salgueiro, S.Mendes, L.O.Martins, C.Frazao, S.Todorovic, E.Moe. Biochemical, Biophysical, and Structural Analysis of An Unusual Dyp From the Extremophile Deinococcus Radiodurans. Molecules V. 29 2024.
ISSN: ESSN 1420-3049
PubMed: 38257271
DOI: 10.3390/MOLECULES29020358