Sodium in PDB 6j3b: Crystal Structure of Human Dhodh in Complex with Inhibitor 1289

All present enzymatic activity of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289:
1.3.5.2;

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289, PDB code: 6j3b was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 1.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.829, 90.829, 122.754, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 17.6

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289 also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289 (pdb code 6j3b). 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 Human Dhodh in Complex with Inhibitor 1289, PDB code: 6j3b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289


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 Human Dhodh in Complex with Inhibitor 1289 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na422 b:37.5 occ:1.00 H A:LYS227 2.4 45.0 1.0 OD2 A:ASP267 2.6 18.2 1.0 HA2 A:GLY226 2.6 37.4 1.0 O A:HOH527 2.8 42.0 1.0 N A:LYS227 3.0 37.5 1.0 HB2 A:LYS227 3.2 22.9 1.0 HB2 A:ASP267 3.2 16.5 1.0 HA A:ASP264 3.3 16.1 1.0 CA A:GLY226 3.5 31.1 1.0 CG A:ASP267 3.5 14.4 1.0 HB3 A:ASP267 3.5 16.5 1.0 CB A:ASP267 3.6 13.8 1.0 C A:GLY226 3.7 36.4 1.0 OD1 A:ASP264 3.7 25.1 1.0 HA3 A:GLY226 3.8 37.4 1.0 CB A:LYS227 3.9 19.1 1.0 CA A:LYS227 4.0 26.6 1.0 HG3 A:GLN263 4.2 27.6 1.0 O A:HOH581 4.2 35.9 1.0 HB3 A:LYS227 4.2 22.9 1.0 HA A:LYS227 4.2 31.9 1.0 CA A:ASP264 4.3 13.4 1.0 O A:GLN225 4.4 24.2 1.0 N A:GLY226 4.6 29.9 1.0 OD1 A:ASP267 4.7 16.9 1.0 O A:GLN263 4.7 15.3 1.0 CG A:ASP264 4.7 24.6 1.0 N A:ASP264 4.9 12.9 1.0 O A:GLY226 4.9 28.1 1.0 C A:GLN225 4.9 25.9 1.0 O A:ASP264 4.9 13.9 1.0 CB A:ASP264 5.0 15.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289


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 Human Dhodh in Complex with Inhibitor 1289 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na423 b:14.3 occ:1.00 H A:GLY334 2.0 10.1 1.0 H A:VAL336 2.1 9.2 1.0 HA A:LEU355 2.6 10.1 1.0 O2P A:FMN403 2.7 7.2 1.0 HB A:VAL336 2.7 12.1 1.0 O A:GLN354 2.7 8.9 1.0 N A:GLY334 2.8 8.4 1.0 HG23 A:VAL336 2.9 13.2 1.0 N A:VAL336 3.0 7.7 1.0 HG23 A:VAL333 3.1 9.7 0.7 H A:GLY335 3.2 9.0 1.0 N A:GLY335 3.3 7.5 1.0 HA A:VAL333 3.3 12.0 0.7 C A:GLY334 3.3 8.5 1.0 CB A:VAL336 3.4 10.1 1.0 HA A:VAL333 3.4 11.2 0.3 CA A:GLY334 3.4 9.2 1.0 CG2 A:VAL336 3.5 11.0 1.0 CA A:LEU355 3.5 8.4 1.0 HB3 A:LEU355 3.5 12.6 1.0 HA2 A:GLY334 3.6 11.1 1.0 HG13 A:VAL333 3.6 11.3 0.3 P A:FMN403 3.7 9.5 1.0 O5' A:FMN403 3.7 7.0 1.0 HG21 A:VAL336 3.7 13.2 1.0 C A:GLN354 3.7 10.0 1.0 CA A:VAL336 3.7 9.5 1.0 O A:HOH591 3.8 8.7 1.0 HG12 A:VAL333 3.8 11.3 0.3 HG22 A:VAL333 3.8 9.7 0.7 CG2 A:VAL333 3.9 8.1 0.7 C A:VAL333 3.9 8.6 0.7 CB A:LEU355 3.9 10.5 1.0 C A:VAL333 3.9 7.2 0.3 HB2 A:LEU355 3.9 12.6 1.0 O A:GLY334 3.9 8.8 1.0 C A:GLY335 4.0 10.2 1.0 CA A:VAL333 4.0 10.0 0.7 O3P A:FMN403 4.1 8.9 1.0 H A:TYR356 4.1 10.9 1.0 N A:LEU355 4.1 9.7 1.0 CA A:GLY335 4.1 8.0 1.0 CA A:VAL333 4.1 9.3 0.3 CG1 A:VAL333 4.1 9.4 0.3 O A:VAL336 4.3 10.1 1.0 HG22 A:VAL336 4.3 13.2 1.0 HA3 A:GLY334 4.4 11.1 1.0 HE2 A:LYS345 4.4 15.8 1.0 HA2 A:GLY335 4.5 9.6 1.0 CB A:VAL333 4.5 9.3 0.7 HA A:VAL336 4.5 11.4 1.0 C A:VAL336 4.5 11.9 1.0 C A:LEU355 4.6 8.8 1.0 HG21 A:VAL333 4.6 9.7 0.7 N A:TYR356 4.6 9.1 1.0 CG1 A:VAL336 4.7 11.1 1.0 HB A:VAL333 4.8 11.2 0.7 CB A:VAL333 4.8 6.9 0.3 H A:GLN354 4.8 10.3 1.0 C5' A:FMN403 4.9 7.2 1.0 HG11 A:VAL336 4.9 13.3 1.0 H5'1 A:FMN403 4.9 8.6 1.0 HA3 A:GLY335 4.9 9.6 1.0 H A:LEU355 4.9 11.6 1.0 HG11 A:VAL333 5.0 11.3 0.3 HG12 A:VAL336 5.0 13.3 1.0

T.Zeng, Z.Zuo, Y.Luo, Y.Zhao, Y.Yu, Q.Chen. A Novel Series of Human Dihydroorotate Dehydrogenase Inhibitors Discovered By in Vitro Screening: Inhibition Activity and Crystallographic Binding Mode. Febs Open Bio V. 9 1348 2019.
ISSN: ESSN 2211-5463
PubMed: 31087527
DOI: 10.1002/2211-5463.12658