Sodium in PDB 9kws: D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans

All present enzymatic activity of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans:
1.7.2.1;

The structure of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 9kws was solved by Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.26 / 1.05
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.038, 115.038, 84.403, 90, 90, 120
R / Rfree (%)	9 / 10.1

The structure of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Copper	(Cu)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 9kws). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 9kws:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:20.8 occ:0.63 O A:HOH795 1.4 16.0 0.3 O A:HOH639 1.9 16.3 1.0 NA A:NA410 1.9 27.1 0.3 OE2 A:GLU239 2.1 13.9 0.8 O A:HOH882 2.4 50.1 1.0 O A:HOH516 2.6 27.2 1.0 OE2 A:GLU239 2.7 12.8 0.2 O A:HOH708 2.8 25.4 0.3 CD A:GLU239 2.9 11.2 0.8 CD A:GLU239 3.0 11.6 0.2 OE1 A:GLU239 3.0 11.9 0.2 OE1 A:GLU239 3.0 11.9 0.8 HD2 A:PRO191 3.2 11.7 1.0 HD3 A:PRO191 3.2 11.7 0.6 HE2 A:HIS298 3.4 10.6 1.0 O A:HOH708 3.4 22.5 0.7 O A:HOH824 3.4 33.7 1.0 HG11 A:VAL190 3.5 14.2 0.8 HA A:VAL190 3.6 11.2 1.0 CD A:PRO191 3.6 9.7 1.0 O A:HOH797 4.1 26.7 1.0 HG3 A:GLU239 4.1 12.3 0.2 CG A:GLU239 4.2 10.2 0.2 NE2 A:HIS298 4.2 8.8 1.0 HB A:VAL190 4.3 12.8 1.0 CG A:GLU239 4.4 9.7 0.8 HG3 A:PRO191 4.4 12.6 1.0 CG1 A:VAL190 4.4 11.9 1.0 CA A:VAL190 4.4 9.4 1.0 HG2 A:GLU239 4.5 12.3 0.2 HG3 A:GLU239 4.5 11.7 0.8 CG A:PRO191 4.6 10.5 1.0 CB A:VAL190 4.6 10.7 1.0 HG2 A:GLU239 4.6 11.7 0.8 H1 A:HOH517 4.7 21.2 1.0 HE1 A:HIS298 4.7 10.7 1.0 HG13 A:VAL190 4.8 14.2 1.0 N A:PRO191 4.8 9.0 1.0 HG2 A:PRO191 4.9 12.6 1.0 CE1 A:HIS298 4.9 8.9 1.0 O A:HOH852 4.9 10.4 0.2

Sodium binding site 2 out of 2 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:27.1 occ:0.35 O A:HOH708 0.9 25.4 0.3 O A:HOH708 1.6 22.5 0.7 O A:HOH795 1.8 16.0 0.3 OE2 A:GLU239 1.8 12.8 0.2 OE2 A:GLU239 1.9 13.9 0.8 NA A:NA409 1.9 20.8 0.6 CD A:GLU239 2.8 11.6 0.2 HD3 A:PRO191 2.9 11.7 0.6 CD A:GLU239 2.9 11.2 0.8 O A:HOH797 3.0 26.7 1.0 O A:HOH824 3.1 33.7 1.0 O A:HOH516 3.2 27.2 1.0 OE1 A:GLU239 3.4 11.9 0.2 OE1 A:GLU239 3.4 11.9 0.8 HA A:VAL190 3.5 11.2 1.0 O A:HOH639 3.7 16.3 1.0 O A:HOH882 3.7 50.1 1.0 HD2 A:PRO191 3.7 11.7 1.0 CD A:PRO191 3.7 9.7 1.0 HG2 A:GLU239 3.9 12.3 0.2 CG A:GLU239 3.9 10.2 0.2 HG2 A:GLU239 4.0 11.7 0.8 HB3 A:ASN238 4.1 9.7 0.9 HB2 A:ASN238 4.1 9.7 0.6 CG A:GLU239 4.1 9.7 0.8 O A:GLY189 4.1 11.2 1.0 OH A:TYR178 4.1 8.7 1.0 HG3 A:GLU239 4.2 12.3 0.2 O A:HOH571 4.3 12.4 1.0 H2 A:HOH571 4.4 14.9 1.0 HG11 A:VAL190 4.4 14.2 0.8 CA A:VAL190 4.5 9.4 1.0 HG3 A:PRO191 4.5 12.6 1.0 HD22 A:ASN238 4.5 10.6 0.9 O A:HOH769 4.5 16.1 1.0 HE2 A:TYR178 4.5 10.3 1.0 CB A:ASN238 4.5 8.1 1.0 HG3 A:GLU239 4.5 11.7 0.8 HH A:TYR178 4.6 10.4 1.0 N A:PRO191 4.7 9.0 1.0 CG A:PRO191 4.7 10.5 1.0 HE2 A:HIS298 4.8 10.6 1.0 H1 A:HOH571 5.0 14.9 1.0 C A:GLY189 5.0 9.4 1.0 HA A:GLU239 5.0 9.2 0.8

Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada. Structural Basis of Cuproenzyme Nitrite Reduction at the Level of A Single Hydrogen Atom. J.Biol.Chem. 10290 2025.
ISSN: ESSN 1083-351X
PubMed: 40436316
DOI: 10.1016/J.JBC.2025.110290