Sodium in PDB 6ep8: Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis

All present enzymatic activity of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis:
1.3.1.9;

The structure of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis, PDB code: 6ep8 was solved by T.Wagner, B.Voegeli, R.G.Rosenthal, G.Stoffel, S.Shima, P.Kiefer, N.Cortina, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.55 / 1.80
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.273, 98.273, 139.836, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 17.5

The binding sites of Sodium atom in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis (pdb code 6ep8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis, PDB code: 6ep8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:35.8 occ:1.00 O A:HOH595 2.3 45.1 1.0 O A:HOH598 2.4 50.9 1.0 O A:HOH605 2.5 55.1 1.0 O A:ALA226 2.5 26.3 1.0 O A:ASP223 2.6 33.0 1.0 O A:GLN224 2.8 36.0 1.0 C A:GLN224 3.4 29.8 1.0 C A:ALA226 3.6 24.8 1.0 C A:ASP223 3.7 30.9 1.0 CA A:GLN224 3.8 28.7 1.0 O A:HOH523 3.9 49.0 1.0 N A:ALA226 4.0 25.0 1.0 C A:ARG225 4.2 27.1 1.0 N A:GLY229 4.2 28.9 1.0 N A:GLN224 4.3 27.0 1.0 N A:ARG225 4.3 26.8 1.0 CA A:ALA226 4.3 24.3 1.0 CA A:GLY229 4.3 30.1 1.0 N A:PRO227 4.6 24.7 1.0 CA A:PRO227 4.6 27.2 1.0 O A:ARG225 4.7 27.7 1.0 CB A:ALA226 4.7 23.9 1.0 C A:PRO227 4.7 26.1 1.0 CA A:ARG225 4.8 26.6 1.0 O A:PRO227 4.9 28.8 1.0 OD1 A:ASP223 5.0 28.1 1.0 CA A:ASP223 5.0 27.9 1.0

Sodium binding site 2 out of 4 in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:49.0 occ:1.00 O A:SER19 2.9 31.0 1.0 O A:HOH529 3.1 72.8 1.0 O A:HOH545 3.1 41.4 1.0 NE2 A:HIS24 3.6 39.8 1.0 O A:HOH563 3.6 44.5 1.0 C A:SER19 3.7 29.2 1.0 CA A:SER19 3.8 28.6 1.0 CG2 A:ILE194 3.8 31.0 1.0 CB A:SER19 3.8 37.1 1.0 CD2 A:HIS24 3.9 33.4 1.0 CB A:ALA235 4.0 32.2 1.0 O A:ARG195 4.4 37.9 1.0 CE1 A:HIS24 4.6 38.0 1.0 N A:ALA235 4.7 27.9 1.0 C A:ARG195 4.8 40.1 1.0 OG A:SER19 4.9 43.5 1.0 CA A:ALA235 4.9 28.3 1.0 N A:SER20 5.0 29.0 1.0

Sodium binding site 3 out of 4 in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:41.5 occ:1.00 O A:HOH480 2.3 44.3 1.0 NE2 A:GLN30 2.9 35.9 1.0 N A:LEU36 3.0 33.3 1.0 O A:LYS57 3.2 51.9 1.0 O A:ALA34 3.7 35.5 1.0 CA A:GLN35 3.7 33.6 0.5 CA A:GLN35 3.7 33.6 0.5 CB A:LEU36 3.7 30.3 1.0 CD A:GLN30 3.7 39.5 1.0 CG A:GLN30 3.8 35.3 1.0 C A:GLN35 3.8 38.4 0.5 C A:GLN35 3.8 38.1 0.5 CA A:LEU36 3.9 31.2 1.0 CG A:LEU36 3.9 36.1 1.0 CB A:ALA56 4.1 47.4 1.0 O A:LEU36 4.2 36.6 1.0 CB A:ALA58 4.2 45.1 1.0 C A:LYS57 4.3 46.7 1.0 C A:LEU36 4.5 36.3 1.0 C A:ALA34 4.5 38.6 1.0 N A:GLN35 4.6 32.7 0.5 N A:GLN35 4.6 32.7 0.5 CD1 A:LEU36 4.7 30.1 1.0 CA A:ALA58 4.7 44.2 1.0 CB A:GLN35 4.7 35.9 0.5 CB A:GLN35 4.7 35.7 0.5 O A:ALA56 4.8 40.1 1.0 C A:ALA56 4.8 41.1 1.0 OE1 A:GLN30 4.8 38.1 1.0 CG A:GLN35 4.9 40.4 0.5 CB A:GLN30 5.0 35.4 1.0 N A:ALA58 5.0 45.7 1.0 CD2 A:LEU36 5.0 33.5 1.0

Sodium binding site 4 out of 4 in the Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Inha Y158F Mutant in Complex with Nadh From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:69.9 occ:1.00 OE2 A:GLU68 2.3 69.9 1.0 O A:HOH548 2.8 50.0 1.0 O A:HOH601 2.8 54.7 1.0 OE1 A:GLU68 2.9 71.2 1.0 CD A:GLU68 2.9 69.4 1.0 O A:HOH461 3.0 35.6 1.0 CD1 A:LEU71 3.6 35.5 1.0 O2 A:GOL310 3.7 92.2 1.0 CE2 A:TYR125 3.8 32.6 1.0 C2 A:GOL310 3.8 91.2 1.0 OG A:SER129 3.9 39.2 1.0 OH A:TYR125 4.0 31.8 1.0 CG A:GLU68 4.4 61.9 1.0 C3 A:GOL310 4.4 93.3 1.0 CZ A:TYR125 4.4 31.4 1.0 O A:HOH416 4.5 43.8 1.0 CB A:SER129 4.6 36.3 1.0 O A:HOH434 4.8 44.8 1.0 CD2 A:TYR125 4.8 29.7 1.0 O A:HOH487 4.9 34.7 1.0 NE2 A:HIS121 4.9 30.6 1.0 O A:VAL65 5.0 32.4 1.0 CG A:LEU71 5.0 30.8 1.0

B.Vogeli, R.G.Rosenthal, G.M.M.Stoffel, T.Wagner, P.Kiefer, N.S.Cortina, S.Shima, T.J.Erb. Inha, the Enoyl-Thioester Reductase Frommycobacterium Tuberculosisforms A Covalent Adduct During Catalysis. J. Biol. Chem. V. 293 17200 2018.
ISSN: ESSN 1083-351X
PubMed: 30217823
DOI: 10.1074/JBC.RA118.005405