Sodium in PDB 7pux: Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2

All present enzymatic activity of Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2:
3.6.4.6;

The structure of Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2, PDB code: 7pux was solved by S.Bothe, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.87 / 1.73
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	146.234, 146.234, 84.397, 90, 90, 120
R / Rfree (%)	19.2 / 23.5

The structure of Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2 (pdb code 7pux). 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 Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2, PDB code: 7pux:

Sodium binding site 1 out of 1 in the Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of P97 N-D1(L198W) in Complex with Fragment TROLL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na520 b:86.3 occ:1.00 O A:GLU194 2.4 40.9 1.0 OE2 A:GLU196 2.4 26.6 1.0 O A:HOH820 2.4 36.5 1.0 O A:ARG191 2.5 35.7 1.0 O A:HOH779 2.5 61.2 1.0 O A:HOH747 2.7 35.4 1.0 HG2 A:ARG191 3.1 35.9 1.0 O A:HOH616 3.2 29.9 1.0 HG3 A:GLU196 3.5 34.9 1.0 C A:GLU194 3.5 39.3 1.0 H A:GLU196 3.5 34.0 1.0 CD A:GLU196 3.5 28.9 1.0 HG3 A:ARG191 3.6 35.9 1.0 C A:ARG191 3.6 35.6 1.0 HA A:GLU192 3.7 49.5 1.0 HA A:GLU195 3.7 42.6 1.0 H A:GLU194 3.7 36.8 1.0 CG A:ARG191 3.7 29.7 1.0 O A:HOH842 4.0 41.9 1.0 CG A:GLU196 4.0 28.9 1.0 N A:GLU196 4.2 28.2 1.0 N A:GLU195 4.4 38.3 1.0 HB2 A:GLU194 4.4 45.2 1.0 CA A:GLU192 4.4 41.0 1.0 CA A:GLU195 4.4 35.3 1.0 N A:GLU194 4.4 30.5 1.0 N A:GLU192 4.4 36.0 1.0 CA A:GLU194 4.5 36.2 1.0 HA A:ARG191 4.5 31.5 1.0 O A:GLU196 4.5 26.7 1.0 CA A:ARG191 4.5 26.1 1.0 HG2 A:GLU196 4.6 34.9 1.0 OE1 A:GLU196 4.6 26.8 1.0 HD2 A:ARG191 4.6 32.8 1.0 O A:HOH673 4.7 29.2 1.0 C A:GLU192 4.7 48.7 1.0 CB A:ARG191 4.7 27.0 1.0 C A:GLU195 4.8 37.3 1.0 CD A:ARG191 4.8 27.1 1.0 O A:GLU192 4.8 57.2 1.0 CB A:GLU194 4.9 37.5 1.0 HB3 A:ARG191 5.0 32.6 1.0

S.Bothe, P.Hanzelmann, S.Bohler, J.Kehrein, M.Zehe, C.Wiedemann, U.A.Hellmich, R.Brenk, H.Schindelin, C.Sotriffer. Fragment Screening Using Biolayer Interferometry Reveals Ligands Targeting the Shp-Motif Binding Site of the Aaa+ Atpase P97 Commun Chem V. 5 169 2022.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-022-00782-5