Sodium in PDB 6kmm: Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis

The structure of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 6kmm was solved by P.Dhankhar, V.Dalal, J.K.Mahto, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.91 / 1.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	79.837, 101.905, 105.405, 88.00, 76.43, 83.28
R / Rfree (%)	16.1 / 20.2

The structure of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis (pdb code 6kmm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis, PDB code: 6kmm:

Sodium binding site 1 out of 1 in the Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hepes Bound Dye Decolorizing Peroxidase From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:48.2 occ:1.00 N B:GLY294 2.8 30.4 1.0 OG1 B:THR292 3.2 29.5 1.0 O C:HOH815 3.4 53.2 1.0 CE B:MET302 3.6 41.2 1.0 CB B:THR292 3.6 28.7 1.0 C B:THR292 3.6 29.7 1.0 CA B:GLY294 3.6 30.9 1.0 N B:GLU293 3.6 30.1 1.0 CD C:LYS167 3.6 26.3 1.0 O B:THR292 3.7 28.7 1.0 CE1 C:TYR25 3.7 25.5 1.0 C B:GLU293 3.8 31.2 1.0 CA B:GLU293 3.9 31.3 1.0 CG C:LYS167 4.1 27.6 1.0 CE C:LYS167 4.2 27.8 1.0 CA B:THR292 4.2 27.4 1.0 CG1 C:VAL165 4.3 26.1 1.0 CD1 C:TYR25 4.4 26.0 1.0 CB C:LYS167 4.4 27.5 1.0 CZ C:TYR25 4.5 25.1 1.0 O C:VAL165 4.6 25.3 1.0 OH C:TYR25 4.6 26.8 1.0 NZ C:LYS167 4.6 29.6 1.0 C B:GLY294 4.7 33.6 1.0 SD B:MET302 4.8 44.3 1.0 O B:GLY294 4.8 33.2 1.0 CG2 B:THR292 4.8 27.6 1.0 N C:LYS167 4.9 26.9 1.0 O C:HOH750 4.9 49.6 1.0 O B:GLU293 5.0 33.7 1.0 CB C:VAL165 5.0 27.8 1.0

P.Dhankhar, V.Dalal, J.K.Mahto, B.R.Gurjar, S.Tomar, A.K.Sharma, P.Kumar. Characterization of Dye-Decolorizing Peroxidase From Bacillus Subtilis. Arch.Biochem.Biophys. V. 693 08590 2020.
ISSN: ESSN 1096-0384
PubMed: 32971035
DOI: 10.1016/J.ABB.2020.108590