Sodium in PDB 6xdf: Crystal Structure of IRE1A in Complex with G-4100

All present enzymatic activity of Crystal Structure of IRE1A in Complex with G-4100:
2.7.11.1;

The structure of Crystal Structure of IRE1A in Complex with G-4100, PDB code: 6xdf was solved by S.Steinbacher, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.33 / 2.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.919, 72.767, 120.054, 90, 129.73, 90
R / Rfree (%)	20.7 / 26.3

The structure of Crystal Structure of IRE1A in Complex with G-4100 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of IRE1A in Complex with G-4100 (pdb code 6xdf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of IRE1A in Complex with G-4100, PDB code: 6xdf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of IRE1A in Complex with G-4100


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 IRE1A in Complex with G-4100 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:79.1 occ:1.00 O A:HOH1150 2.5 49.3 1.0 O A:VAL625 2.8 45.5 1.0 O A:HIS622 2.9 39.6 1.0 C A:HIS622 3.8 37.6 1.0 N A:ARG627 4.0 53.2 1.0 CB A:ARG627 4.0 62.3 1.0 OE2 B:GLU621 4.0 114.3 1.0 C A:VAL625 4.1 43.9 1.0 CA A:PRO623 4.1 34.5 1.0 CA A:ARG627 4.2 53.1 1.0 O A:PRO623 4.3 50.0 1.0 N A:HIS622 4.3 46.0 1.0 C A:PRO623 4.4 39.9 1.0 C A:ILE626 4.4 38.2 1.0 N A:PRO623 4.4 35.0 1.0 CG A:ARG627 4.5 69.2 1.0 OE1 A:GLU643 4.5 69.5 1.0 CD A:ARG627 4.8 66.8 1.0 O A:ILE626 4.8 42.1 1.0 CA A:HIS622 4.8 35.8 1.0 CA A:ILE626 4.9 44.8 1.0 N A:ILE626 4.9 41.8 1.0 N A:VAL625 4.9 38.6 1.0 CB A:GLU621 5.0 62.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of IRE1A in Complex with G-4100


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 IRE1A in Complex with G-4100 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1001 b:68.7 occ:1.00 O B:VAL625 2.7 52.9 1.0 O B:ASP620 2.8 50.4 1.0 O B:HIS622 2.8 47.0 1.0 OE2 A:GLU621 3.5 91.5 1.0 C B:HIS622 3.8 44.3 1.0 C B:VAL625 3.9 43.5 1.0 C B:ASP620 4.0 59.3 1.0 N B:ARG627 4.1 50.0 1.0 CB B:ARG627 4.2 69.0 1.0 O B:PRO623 4.2 52.0 1.0 CA B:PRO623 4.2 47.4 1.0 C B:ILE626 4.2 46.8 1.0 CA B:ARG627 4.2 61.7 1.0 C B:PRO623 4.3 50.1 1.0 N B:PRO623 4.5 39.8 1.0 CD A:GLU621 4.5 111.5 1.0 CG B:ARG627 4.5 79.7 1.0 O B:ILE626 4.5 49.7 1.0 O B:GLU621 4.6 64.0 1.0 C B:GLU621 4.6 61.4 1.0 N B:VAL625 4.7 45.7 1.0 CA B:ASP620 4.7 66.3 1.0 N B:HIS622 4.7 48.9 1.0 OE1 A:GLU621 4.7 111.6 1.0 CA B:ILE626 4.7 51.2 1.0 N B:ILE626 4.8 47.3 1.0 CD B:ARG627 4.8 91.3 1.0 CA B:VAL625 4.8 42.5 1.0 CB B:ASP620 4.8 62.1 1.0 OE1 B:GLU643 4.9 48.9 1.0 CA B:HIS622 4.9 44.3 1.0 N B:GLU621 4.9 58.3 1.0

R.E.Beveridge, H.A.Wallweber, A.Ashkenazi, M.Beresini, K.R.Clark, P.Gibbons, E.Ghiro, S.Kaufman, A.Larivee, M.Leblanc, J.P.Leclerc, A.Lemire, C.Ly, J.Rudolph, J.B.Schwarz, S.Srivastava, W.Wang, L.Zhao, M.G.Braun. Identification of Braf-Sparing Amino-Thienopyrimidines with Potent IRE1 Alpha Inhibitory Activity. Acs Med.Chem.Lett. V. 11 2389 2020.
ISSN: ISSN 1948-5875
PubMed: 33335661
DOI: 10.1021/ACSMEDCHEMLETT.0C00344