Sodium in PDB 7a76: Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus

All present enzymatic activity of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus:
1.8.1.9;

The structure of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus, PDB code: 7a76 was solved by M.Hammerstad, I.Gudim, H.-P.Hersleth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.23 / 1.65
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.731, 114.9, 146.73, 90, 90, 90
R / Rfree (%)	19 / 21.8

The binding sites of Sodium atom in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus (pdb code 7a76). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus, PDB code: 7a76:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.3 occ:1.00 O A:HOH591 3.1 28.1 1.0 N A:ARG192 3.2 27.5 1.0 CZ A:ARG192 3.6 67.8 1.0 CG A:ARG192 3.7 43.8 1.0 CA A:TYR191 3.8 22.7 1.0 NH1 A:ARG192 3.8 64.4 1.0 NE A:ARG192 3.8 65.1 1.0 CA A:GLY168 3.8 22.4 1.0 CD1 A:TYR191 3.8 28.6 1.0 NH2 A:ARG192 3.9 70.8 1.0 N A:GLY168 3.9 20.3 1.0 CB A:ARG192 3.9 36.4 1.0 C A:TYR191 4.0 26.6 1.0 O A:LEU190 4.1 22.9 1.0 CG2 A:ILE167 4.2 23.2 1.0 CA A:ARG192 4.2 28.3 1.0 CD A:ARG192 4.3 58.4 1.0 O A:HOH679 4.5 32.9 1.0 CE1 A:TYR191 4.6 30.9 1.0 C A:GLY168 4.6 24.6 1.0 O A:HOH666 4.6 37.1 1.0 N A:TYR191 4.6 22.0 1.0 CB A:TYR191 4.7 23.3 1.0 CG A:TYR191 4.7 28.4 1.0 C A:LEU190 4.8 21.0 1.0 C A:ILE167 4.8 23.1 1.0 N A:GLY169 4.9 29.7 1.0 O A:ALA223 5.0 31.3 1.0

Sodium binding site 2 out of 4 in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:22.8 occ:1.00 N B:ARG192 3.3 30.4 1.0 O B:HOH577 3.3 26.9 1.0 NH1 B:ARG192 3.3 69.7 1.0 CZ B:ARG192 3.5 60.6 1.0 CG B:ARG192 3.6 42.6 1.0 CD1 B:TYR191 3.8 29.3 1.0 CA B:GLY168 3.8 23.1 1.0 CA B:TYR191 3.8 24.2 1.0 N B:GLY168 3.9 21.6 1.0 CB B:ARG192 3.9 34.9 1.0 NE B:ARG192 4.0 62.1 1.0 NH2 B:ARG192 4.0 61.8 1.0 C B:TYR191 4.0 25.6 1.0 CG2 B:ILE167 4.1 22.9 1.0 O B:LEU190 4.1 28.5 1.0 CA B:ARG192 4.2 31.5 1.0 CD B:ARG192 4.3 51.0 1.0 CE1 B:TYR191 4.5 34.4 1.0 C B:GLY168 4.5 29.2 1.0 O B:HOH653 4.6 30.9 1.0 N B:TYR191 4.7 26.2 1.0 CG B:TYR191 4.7 32.0 1.0 CB B:TYR191 4.7 32.7 1.0 NZ B:LYS170 4.8 36.8 1.0 C B:ILE167 4.8 24.2 1.0 C B:LEU190 4.8 24.1 1.0 N B:GLY169 4.8 29.4 1.0 CG2 B:THR253 5.0 28.0 0.5

Sodium binding site 3 out of 4 in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:26.9 occ:1.00 NE C:ARG192 3.1 48.1 1.0 O C:HOH659 3.1 43.7 1.0 O C:HOH560 3.2 34.2 1.0 N C:ARG192 3.3 37.1 1.0 NH2 C:ARG192 3.7 45.9 1.0 CD1 C:TYR191 3.7 31.6 1.0 CA C:GLY168 3.7 29.9 1.0 N C:GLY168 3.7 26.4 1.0 CA C:TYR191 3.8 30.2 1.0 CZ C:ARG192 3.8 57.1 1.0 CG C:ARG192 3.8 35.7 1.0 CG2 C:ILE167 3.8 31.1 1.0 CB C:ARG192 3.9 36.3 1.0 C C:TYR191 4.0 31.5 1.0 O C:LEU190 4.0 27.9 1.0 CD C:ARG192 4.0 43.6 1.0 CA C:ARG192 4.2 39.1 1.0 CE1 C:TYR191 4.4 34.2 1.0 C C:GLY168 4.5 31.4 1.0 CG C:TYR191 4.6 38.0 1.0 C C:ILE167 4.6 28.8 1.0 CB C:TYR191 4.6 34.9 1.0 N C:TYR191 4.7 28.5 1.0 O C:HOH622 4.7 37.0 1.0 C C:LEU190 4.7 25.3 1.0 CG2 C:THR253 4.8 41.3 1.0 O C:HOH630 5.0 35.7 1.0 N C:GLY169 5.0 30.3 1.0

Sodium binding site 4 out of 4 in the Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bacillithiol Disulfide Reductase Bdr (Ypda) From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:29.9 occ:1.00 N D:ARG192 3.2 46.5 1.0 NH1 D:ARG192 3.6 76.0 1.0 CA D:TYR191 3.7 41.8 1.0 CD1 D:TYR191 3.7 47.8 1.0 N D:GLY168 3.8 34.7 1.0 CG D:ARG192 3.8 57.2 1.0 C D:TYR191 3.9 45.1 1.0 CA D:GLY168 3.9 35.1 1.0 CD D:ARG192 3.9 72.3 1.0 CB D:ARG192 3.9 51.2 1.0 CG2 D:ILE167 4.0 37.0 1.0 O D:LEU190 4.0 37.2 1.0 CA D:ARG192 4.1 50.0 1.0 O D:HOH624 4.4 40.6 1.0 CE1 D:TYR191 4.4 50.2 1.0 C D:GLY168 4.5 36.1 1.0 N D:TYR191 4.6 40.7 1.0 O D:HOH582 4.6 41.7 1.0 CB D:TYR191 4.6 43.7 1.0 CZ D:ARG192 4.6 74.8 1.0 CG D:TYR191 4.6 42.3 1.0 C D:LEU190 4.7 38.4 1.0 NE D:ARG192 4.7 76.4 1.0 N D:GLY169 4.8 39.3 1.0 C D:ILE167 4.8 33.0 1.0 O D:ALA223 4.9 48.5 1.0 CG2 D:THR253 4.9 46.6 1.0

M.Hammerstad, I.Gudim, H.P.Hersleth. The Crystal Structures of Bacillithiol Disulfide Reductase Bdr (Ypda) Provide Structural and Functional Insight Into A New Type of Fad-Containing Nadph-Dependent Oxidoreductase. Biochemistry V. 59 4793 2020.
ISSN: ISSN 0006-2960
PubMed: 33326741
DOI: 10.1021/ACS.BIOCHEM.0C00745