Sodium in PDB 7o9j: Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen

The structure of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen, PDB code: 7o9j was solved by A.Rai, R.Fedorov, D.J.Manstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.25 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.03, 141.03, 95.56, 90, 90, 90
R / Rfree (%)	14.6 / 16.5

The structure of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen (pdb code 7o9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen, PDB code: 7o9j:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen


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 Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:31.1 occ:1.00 O B:HOH629 2.7 19.7 1.0 O B:HOH550 2.7 23.5 1.0 N A:ASP109 3.1 18.6 1.0 CG A:ASP109 3.2 25.3 1.0 OD1 A:ASP109 3.4 21.9 1.0 CB A:ASP109 3.5 19.3 1.0 OH B:TYR13 3.5 21.4 1.0 N A:MET108 3.6 17.6 1.0 OD2 A:ASP109 3.6 23.6 1.0 NH2 A:ARG107 3.8 24.1 1.0 CA A:ASP109 3.9 17.9 1.0 CB A:ARG107 3.9 17.2 1.0 NE A:ARG107 4.1 22.9 1.0 CZ A:ARG107 4.1 28.0 1.0 C A:MET108 4.1 18.2 1.0 CZ B:TYR13 4.1 18.6 1.0 C A:ARG107 4.2 18.8 1.0 CA A:MET108 4.2 18.2 1.0 CA A:ARG107 4.3 18.7 1.0 CD1 B:LEU12 4.3 18.9 1.0 O B:ARG137 4.4 19.2 1.0 CB B:LEU12 4.4 16.7 1.0 CB A:MET108 4.4 19.4 1.0 O A:HOH582 4.6 24.6 1.0 CE2 B:TYR13 4.6 16.6 1.0 CD2 B:LEU12 4.6 21.5 1.0 CG A:ARG107 4.6 20.1 1.0 CG B:LEU12 4.7 18.2 1.0 CE1 B:TYR13 4.9 19.0 1.0 NH1 A:ARG107 4.9 25.7 1.0 CD A:ARG107 5.0 22.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:46.0 occ:1.00 N B:HIS134 3.1 18.4 1.0 O B:HOH565 3.3 22.0 1.0 CA B:ILE133 3.7 18.3 1.0 C B:ILE133 3.9 20.1 1.0 O B:HIS134 4.0 21.9 1.0 CA B:HIS134 4.0 18.0 1.0 CB B:HIS134 4.0 18.9 1.0 CG2 B:ILE133 4.1 22.6 1.0 O B:GLU132 4.1 21.8 1.0 CD1 B:ILE133 4.2 22.9 1.0 OE1 A:GLN246 4.2 38.2 1.0 O B:HOH766 4.3 56.5 1.0 C B:HIS134 4.3 19.8 1.0 CG B:HIS134 4.4 18.3 1.0 CB B:ILE133 4.4 19.3 1.0 CD2 B:TYR244 4.6 19.0 1.0 CB B:TYR244 4.7 17.1 1.0 N B:ILE133 4.8 17.8 1.0 CD2 B:HIS134 4.9 20.3 1.0 C B:GLU132 4.9 21.8 1.0 CG1 B:ILE133 5.0 20.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dyp-Type Peroxidase From Dictyostelium Discoideum in Complex with An Activated Form of Oxygen within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:31.0 occ:1.00 OH A:TYR13 2.7 19.5 1.0 O B:HOH725 2.8 21.9 1.0 O A:HOH584 2.8 29.2 1.0 CA B:ARG107 3.4 17.0 1.0 CB B:ARG107 3.5 18.0 1.0 CZ A:TYR13 3.6 18.9 1.0 CE2 A:TYR13 3.6 17.7 1.0 CG B:ARG107 3.6 18.5 1.0 O B:HOH638 3.8 29.4 1.0 N B:MET108 3.8 17.3 1.0 CD1 A:LEU12 3.9 16.3 1.0 O B:ASP106 4.1 19.2 1.0 C B:ARG107 4.1 18.9 1.0 CZ B:ARG107 4.2 28.6 1.0 NE B:ARG107 4.3 22.1 1.0 O A:ASP106 4.3 19.9 1.0 NH1 B:ARG107 4.4 26.7 1.0 OH B:TYR13 4.5 21.4 1.0 CE2 B:TYR13 4.5 16.6 1.0 O B:HOH550 4.5 23.5 1.0 N B:ARG107 4.5 16.2 1.0 NH2 B:ARG107 4.6 25.0 1.0 CD B:ARG107 4.6 20.9 1.0 O A:HOH613 4.6 18.9 1.0 CZ B:TYR13 4.8 18.6 1.0 CB A:LEU12 4.8 15.3 1.0 C B:ASP106 4.8 19.4 1.0 CE1 A:TYR13 4.9 20.9 1.0 CG A:LEU12 4.9 17.5 1.0 CD2 A:TYR13 5.0 17.4 1.0

A.Rai, J.P.Klare, P.Y.A.Reinke, F.Englmaier, J.Fohrer, R.Fedorov, M.H.Taft, I.Chizhov, U.Curth, O.Plettenburg, D.J.Manstein. Structural and Biochemical Characterization of A Dye-Decolorizing Peroxidase From Dictyostelium Discoideum . Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34200865
DOI: 10.3390/IJMS22126265