Calcium in PDB 8re3: Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3 was solved by B.A.Salgueiro, K.Frade, C.Frazao, P.Matias, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.74 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.09, 97.697, 116.037, 90, 90, 90
R / Rfree (%)	16.7 / 19.5

The structure of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Calcium atom in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans (pdb code 8re3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans, PDB code: 8re3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:21.4 occ:1.00 O A:HOH851 2.4 25.9 1.0 OD1 A:ASP434 2.4 22.2 1.0 OD2 A:ASP434 2.5 23.4 1.0 CG A:ASP434 2.8 24.5 1.0 CB A:ASP434 4.3 23.2 1.0 O A:HOH623 4.4 19.0 1.0 OG A:SER254 4.5 25.1 1.0 OE2 A:GLU415 4.5 68.4 1.0 O A:HOH768 4.6 26.0 1.0 HB3 A:SER254 4.6 29.5 1.0 HB3 A:ASP434 4.7 28.0 1.0 O A:HOH770 4.7 25.1 1.0 HB2 A:ASP434 4.7 28.0 1.0 HA A:ASP434 5.0 26.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Determination of Dye-Decolorizing Peroxidase (Dyp) Mutant M190G From Deinoccoccus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:17.6 occ:1.00 O B:HOH823 2.3 29.1 1.0 OD1 B:ASP434 2.4 20.3 1.0 O B:HOH860 2.5 22.6 1.0 OD2 B:ASP434 2.5 19.1 1.0 CG B:ASP434 2.8 18.8 1.0 CB B:ASP434 4.3 16.6 1.0 O B:HOH638 4.5 19.4 1.0 O B:HOH659 4.5 20.8 1.0 O B:HOH889 4.5 31.8 1.0 OG B:SER254 4.6 20.9 1.0 HB3 B:SER254 4.6 22.8 1.0 HB3 B:ASP434 4.7 20.1 1.0 HB2 B:ASP434 4.7 20.1 1.0 O B:HOH812 4.8 18.6 1.0 OE2 B:GLU415 4.9 63.5 1.0 HA B:ASP434 4.9 19.7 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