Calcium in PDB 8s6c: Crystal Structure of Cyanobacterium TDX16 Peroxidase

All present enzymatic activity of Crystal Structure of Cyanobacterium TDX16 Peroxidase:
1.11.1.7;

The structure of Crystal Structure of Cyanobacterium TDX16 Peroxidase, PDB code: 8s6c was solved by H.J.Rozeboom, S.Savino, M.W.Fraaije, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.91 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.667, 72.541, 56.203, 90, 95.85, 90
R / Rfree (%)	15.1 / 18.8

The structure of Crystal Structure of Cyanobacterium TDX16 Peroxidase also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Cyanobacterium TDX16 Peroxidase (pdb code 8s6c). 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 of Cyanobacterium TDX16 Peroxidase, PDB code: 8s6c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Cyanobacterium TDX16 Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cyanobacterium TDX16 Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:23.0 occ:1.00 O A:LYS352 2.4 23.9 1.0 O A:HOH899 2.4 23.9 1.0 O A:HOH826 2.4 24.1 1.0 O A:THR295 2.4 24.0 1.0 OG1 A:THR295 2.4 23.2 1.0 OD1 A:ASP350 2.4 22.7 1.0 O A:GLU348 2.4 21.1 1.0 C A:THR295 3.3 24.5 1.0 CG A:ASP350 3.4 22.7 1.0 C A:LYS352 3.5 22.2 1.0 CB A:THR295 3.6 24.3 1.0 C A:GLU348 3.6 21.2 1.0 CA A:THR295 3.7 25.5 1.0 OD2 A:ASP350 3.8 22.5 1.0 CA A:LYS352 4.2 24.0 1.0 CB A:LYS352 4.2 25.2 1.0 N A:GLU348 4.2 25.2 1.0 N A:ASP350 4.3 21.9 1.0 N A:LYS352 4.3 22.2 1.0 OE1 A:GLN58 4.3 26.8 1.0 CB A:GLN347 4.3 23.4 1.0 O A:ASP350 4.3 21.5 1.0 CG2 A:THR295 4.4 24.6 1.0 CA A:GLU348 4.5 23.4 1.0 O A:HOH873 4.5 26.7 1.0 N A:ILE353 4.5 23.5 1.0 N A:MET296 4.6 24.4 1.0 N A:ILE349 4.6 23.4 1.0 CB A:ASP350 4.6 23.3 1.0 C A:GLN347 4.6 22.8 1.0 C A:ASP350 4.7 20.4 1.0 CA A:ILE349 4.7 24.2 1.0 CA A:ASP350 4.8 22.7 1.0 C A:ILE349 4.9 24.4 1.0 CA A:ILE353 4.9 26.5 1.0 CB A:GLU348 5.0 25.9 1.0 O A:GLN347 5.0 25.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Cyanobacterium TDX16 Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cyanobacterium TDX16 Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:23.6 occ:1.00 O A:TRP142 2.3 21.6 1.0 O A:ASP82 2.3 23.6 1.0 OG1 A:THR140 2.4 22.2 1.0 OG A:SER146 2.4 22.4 1.0 O A:THR140 2.4 25.9 1.0 OD1 A:ASP82 2.4 22.2 1.0 OD1 A:ASP144 2.4 22.0 1.0 C A:THR140 3.3 25.2 1.0 CB A:SER146 3.4 23.0 1.0 C A:ASP82 3.4 23.0 1.0 CG A:ASP144 3.4 22.4 1.0 C A:TRP142 3.5 23.0 1.0 CG A:ASP82 3.6 25.5 1.0 CB A:THR140 3.6 24.2 1.0 OD2 A:ASP144 3.8 22.3 1.0 CA A:THR140 3.9 22.8 1.0 CA A:ASP82 4.0 23.4 1.0 N A:TRP142 4.0 24.6 1.0 N A:SER146 4.1 22.6 1.0 N A:ASP144 4.2 21.4 1.0 N A:THR140 4.2 21.7 1.0 C A:SER141 4.2 25.7 1.0 CB A:ASP82 4.3 23.0 1.0 CA A:TRP142 4.3 23.3 1.0 CA A:SER146 4.3 21.0 1.0 N A:SER141 4.4 24.0 1.0 O A:SER141 4.5 23.8 1.0 N A:LEU83 4.6 23.4 1.0 N A:ILE143 4.6 21.8 1.0 OD2 A:ASP82 4.6 23.7 1.0 O A:HOH762 4.6 23.1 1.0 CB A:ASP144 4.6 22.9 1.0 CG2 A:THR140 4.7 22.4 1.0 CA A:SER141 4.7 25.0 1.0 CA A:ILE143 4.8 22.3 1.0 CB A:TRP142 4.8 23.0 1.0 CA A:ASP144 4.8 21.5 1.0 CA A:LEU83 4.9 23.9 1.0 N A:ALA145 4.9 20.9 1.0

O.Pecanac, C.Martin, S.Savino, H.J.Rozeboom, M.Fraaije, N.Loncar. Biochemical and Structural Characterisation of A Bacterial Lactoperoxidase. Chembiochem 00713 2024.
ISSN: ESSN 1439-7633
PubMed: 39570012
DOI: 10.1002/CBIC.202400713