Sodium in PDB 6jme: Crystal Structure of Human Dhodh in Complex with Inhibitor 0946

All present enzymatic activity of Crystal Structure of Human Dhodh in Complex with Inhibitor 0946:
1.3.5.2;

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 0946, PDB code: 6jme 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)	41.02 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.605, 90.605, 123.057, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 17

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 0946 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Dhodh in Complex with Inhibitor 0946 (pdb code 6jme). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human Dhodh in Complex with Inhibitor 0946, PDB code: 6jme:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 0946


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 0946 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:27.6 occ:1.00 O A:HOH577 2.8 14.8 1.0 O A:HOH650 2.8 23.4 1.0 O A:GLN165 2.8 14.2 1.0 HB3 A:GLN168 2.8 16.8 1.0 H1 A:ACT405 2.8 33.1 1.0 OXT A:ACT405 2.8 32.0 1.0 HG3 A:GLN165 2.8 20.1 1.0 C A:ACT405 3.2 42.1 1.0 H3 A:ACT405 3.2 33.1 1.0 CH3 A:ACT405 3.2 27.6 1.0 H A:ALA169 3.4 18.4 1.0 HG2 A:GLN165 3.4 20.1 1.0 HA A:GLN165 3.5 17.1 1.0 HB2 A:ALA169 3.5 22.6 1.0 CG A:GLN165 3.6 16.7 1.0 HG3 A:GLN168 3.6 16.4 1.0 N A:ALA169 3.7 15.4 1.0 CB A:GLN168 3.7 14.0 1.0 C A:GLN165 3.7 17.9 1.0 HG2 A:GLN168 3.8 16.4 1.0 HA A:ALA169 3.9 21.2 1.0 CG A:GLN168 3.9 13.7 1.0 HE21 A:GLN165 4.0 29.6 1.0 CA A:GLN165 4.0 14.3 1.0 O A:ACT405 4.1 55.4 1.0 CA A:ALA169 4.1 17.7 1.0 C A:GLN168 4.1 15.6 1.0 H2 A:ACT405 4.3 33.1 1.0 CB A:ALA169 4.3 18.9 1.0 HA A:LEU205 4.3 15.1 1.0 HB2 A:GLN168 4.3 16.8 1.0 CB A:GLN165 4.4 15.5 1.0 O A:LEU205 4.4 16.1 1.0 CA A:GLN168 4.5 14.3 1.0 O A:HOH684 4.5 30.0 1.0 HD23 A:LEU205 4.5 21.1 1.0 NE2 A:GLN165 4.6 24.7 1.0 CD A:GLN165 4.7 24.8 1.0 H A:GLN168 4.7 19.5 1.0 O A:GLN168 4.8 13.8 1.0 HB3 A:ALA169 4.8 22.6 1.0 HA A:GLN166 4.9 23.8 1.0 HB2 A:GLN165 4.9 18.6 1.0 HB1 A:ALA169 4.9 22.6 1.0 N A:GLN166 4.9 18.9 1.0 C A:LEU205 5.0 14.5 1.0 O A:HOH651 5.0 13.4 1.0 N A:GLN168 5.0 16.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 0946


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 0946 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:31.2 occ:1.00 H A:GLN263 2.2 19.8 1.0 HB A:THR261 2.5 25.7 1.0 O A:HOH749 2.6 47.3 1.0 O4 A:SO4410 2.7 58.6 1.0 HB2 A:GLN263 2.9 28.2 1.0 N A:GLN263 3.0 16.5 1.0 HB2 A:SER262 3.0 28.8 1.0 H A:SER262 3.1 23.6 1.0 HB3 A:GLN263 3.2 28.2 1.0 CB A:GLN263 3.4 23.5 1.0 CB A:THR261 3.4 21.4 1.0 N A:SER262 3.4 19.7 1.0 O A:HOH694 3.6 32.5 1.0 HG1 A:THR261 3.6 24.5 1.0 OG1 A:THR261 3.7 20.4 1.0 CA A:GLN263 3.8 17.5 1.0 CB A:SER262 3.9 24.0 1.0 C A:SER262 3.9 13.8 1.0 CA A:SER262 3.9 18.6 1.0 S A:SO4410 4.0 0.0 1.0 C A:THR261 4.1 19.7 1.0 O1 A:SO4410 4.2 39.2 1.0 HG21 A:THR261 4.3 33.5 1.0 HA A:GLN263 4.3 21.0 1.0 CA A:THR261 4.3 19.1 1.0 CG2 A:THR261 4.4 27.9 1.0 HA A:THR261 4.5 22.9 1.0 HB3 A:SER262 4.5 28.8 1.0 H A:ASP264 4.5 18.8 1.0 HG22 A:THR261 4.6 33.5 1.0 OG A:SER262 4.6 31.1 1.0 O2 A:SO4410 4.8 68.0 1.0 CG A:GLN263 4.8 29.1 1.0 HA A:SER262 4.9 22.3 1.0 HG A:SER262 4.9 37.4 1.0 HG2 A:GLN263 4.9 34.9 1.0 O3 A:SO4410 4.9 69.5 1.0 O A:THR261 5.0 17.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 0946


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Dhodh in Complex with Inhibitor 0946 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:47.3 occ:1.00 O A:HOH546 3.1 30.8 1.0 O A:HOH524 3.2 15.4 1.0 O A:ARG249 3.3 18.2 1.0 H A:ARG249 3.5 18.7 1.0 HA A:PRO250 3.6 16.3 1.0 O A:VAL247 3.7 23.0 1.0 HA A:ASP207 3.7 14.7 1.0 C A:ARG249 3.7 16.6 1.0 N A:ARG249 3.8 15.6 1.0 O A:ALA206 4.0 16.0 1.0 HA A:HIS248 4.1 19.1 1.0 O A:HOH684 4.1 30.0 1.0 N A:PRO250 4.2 14.3 1.0 C A:VAL247 4.3 22.3 1.0 C A:HIS248 4.3 13.9 1.0 CA A:PRO250 4.3 13.6 1.0 O A:ACT405 4.4 55.4 1.0 CA A:ARG249 4.4 14.7 1.0 HE1 A:HIS86 4.5 33.7 1.0 OD1 A:ASP207 4.5 20.0 1.0 CA A:HIS248 4.5 15.9 1.0 NE2 A:HIS86 4.6 21.9 1.0 N A:HIS248 4.6 16.4 1.0 CA A:ASP207 4.6 12.3 1.0 HB3 A:PRO250 4.7 16.8 1.0 HA A:VAL247 4.7 20.8 1.0 O A:ARG246 4.8 19.0 1.0 O A:ASP207 4.8 13.2 1.0 CE1 A:HIS86 4.9 28.1 1.0 C A:ALA206 4.9 14.6 1.0 HB3 A:ARG249 5.0 24.8 1.0

Q.Chen, Y.Yu, Q.Chen. N/A N/A.