Sodium in PDB 3wkq: Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate

The structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate, PDB code: 3wkq was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.25 / 1.15
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.981, 114.981, 84.431, 90.00, 90.00, 120.00
R / Rfree (%)	11.8 / 13.7

The structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate also contains other interesting chemical elements:

Copper

(Cu)

6 atoms

The binding sites of Sodium atom in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate (pdb code 3wkq). 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 Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate, PDB code: 3wkq:

Sodium binding site 1 out of 1 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:54.5 occ:1.00 OE2 A:GLU78 2.1 16.4 1.0 O A:HOH683 2.8 35.1 1.0 CD A:GLU78 3.1 11.6 1.0 O A:HOH852 3.4 26.9 0.5 OE1 A:GLU78 3.4 12.7 1.0 O A:HOH638 3.5 15.0 0.5 O A:HOH835 3.7 35.0 1.0 O1 A:FMT416 3.8 24.2 0.5 C A:FMT416 4.1 20.2 0.5 OD1 A:ASN158 4.1 22.4 0.3 CD A:PRO128 4.4 9.3 1.0 CG A:GLU78 4.4 11.5 1.0 O A:ASN126 4.8 12.6 0.5 CG A:PRO128 4.8 10.1 1.0

Y.Fukuda, T.Inoue. Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate To Be Published.