Sodium in PDB 6c9n: Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin

All present enzymatic activity of Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin:
2.7.1.20;

The structure of Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin, PDB code: 6c9n was solved by R.A.Crespo, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.59 / 2.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	48.910, 48.910, 262.059, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.1

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin (pdb code 6c9n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin, PDB code: 6c9n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:40.8 occ:1.00 O A:THR253 2.7 29.4 1.0 O A:ASP251 2.8 31.9 1.0 O A:SER290 2.9 36.1 1.0 HG12 A:VAL287 2.9 36.9 1.0 HG13 A:VAL287 2.9 36.9 1.0 O A:VAL287 3.0 31.8 1.0 O A:THR291 3.0 33.9 1.0 HB3 A:ASP251 3.1 42.1 1.0 CG1 A:VAL287 3.3 30.7 1.0 O A:GLY292 3.4 37.4 1.0 H A:THR253 3.6 39.6 1.0 HB A:THR253 3.6 33.4 1.0 HA A:THR293 3.7 42.1 1.0 C A:ASP251 3.7 33.9 1.0 C A:THR253 3.7 24.2 1.0 N A:THR253 3.7 32.9 1.0 C A:THR291 3.8 31.0 1.0 C A:VAL287 3.8 30.6 1.0 C A:SER290 3.8 36.2 1.0 HG11 A:VAL287 3.9 36.9 1.0 CB A:ASP251 3.9 35.0 1.0 C A:GLY292 4.0 38.2 1.0 HA A:LEU288 4.1 37.7 1.0 OD1 A:ASP251 4.1 35.5 1.0 HA A:THR291 4.1 47.7 1.0 CA A:THR253 4.1 31.9 1.0 C A:PRO252 4.2 31.3 1.0 H A:SER290 4.3 44.7 1.0 HG23 A:VAL255 4.3 37.6 1.0 HG22 A:THR293 4.3 41.5 1.0 CB A:THR253 4.3 27.8 1.0 CA A:THR291 4.4 39.6 1.0 CG A:ASP251 4.4 39.1 1.0 CA A:ASP251 4.4 40.5 1.0 HB2 A:SER290 4.4 53.8 1.0 N A:THR293 4.5 37.1 1.0 CA A:THR293 4.5 35.0 1.0 N A:THR291 4.5 35.7 1.0 N A:PRO252 4.5 31.4 1.0 H A:ASP251 4.5 47.2 1.0 CB A:VAL287 4.5 27.6 1.0 HA A:VAL287 4.6 36.8 1.0 HA A:PRO252 4.6 38.3 1.0 CA A:VAL287 4.6 30.6 1.0 N A:LEU288 4.6 28.4 1.0 N A:GLY292 4.6 33.4 1.0 HB2 A:ASP251 4.7 42.1 1.0 CA A:PRO252 4.7 31.9 1.0 CA A:LEU288 4.7 31.3 1.0 CA A:GLY292 4.8 35.8 1.0 CA A:SER290 4.8 42.8 1.0 HA3 A:GLY254 4.8 38.8 1.0 HA2 A:GLY292 4.9 43.1 1.0 O A:PRO252 4.9 29.6 1.0 HG1 A:THR253 4.9 38.4 1.0 N A:GLY254 4.9 26.3 1.0 N A:SER290 4.9 37.2 1.0 N A:ASP251 4.9 39.3 1.0 O A:LEU288 5.0 33.4 1.0 C A:LEU288 5.0 34.8 1.0 HB A:VAL287 5.0 33.2 1.0 HG22 A:VAL255 5.0 37.6 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mycobacterium Tuberculosis Adenosine Kinase Bound to Sangivamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:42.4 occ:1.00 O B:SER290 2.7 33.7 1.0 O B:ASP251 2.8 32.9 1.0 O B:THR253 2.8 29.7 1.0 O B:VAL287 2.8 31.0 1.0 HG13 B:VAL287 2.9 36.6 1.0 HG12 B:VAL287 3.0 36.6 1.0 O B:THR291 3.0 35.8 1.0 HB3 B:ASP251 3.1 40.8 1.0 CG1 B:VAL287 3.4 30.4 1.0 O B:GLY292 3.5 36.9 1.0 HB B:THR253 3.7 34.7 1.0 H B:THR253 3.7 38.5 1.0 C B:ASP251 3.7 33.6 1.0 HA B:THR293 3.7 40.9 1.0 C B:THR291 3.7 32.8 1.0 C B:SER290 3.7 36.8 1.0 C B:VAL287 3.7 30.2 1.0 C B:THR253 3.9 26.5 1.0 N B:THR253 3.9 32.0 1.0 HG11 B:VAL287 4.0 36.6 1.0 CB B:ASP251 4.0 33.9 1.0 HA B:THR291 4.0 46.4 1.0 C B:GLY292 4.1 41.0 1.0 HA B:LEU288 4.1 37.0 1.0 OD1 B:ASP251 4.1 36.1 1.0 H B:SER290 4.2 43.4 1.0 CA B:THR253 4.3 32.2 1.0 CA B:THR291 4.3 38.6 1.0 C B:PRO252 4.3 33.2 1.0 HG23 B:VAL255 4.4 35.2 1.0 CA B:ASP251 4.4 39.2 1.0 CG B:ASP251 4.4 39.1 1.0 N B:THR291 4.4 34.4 1.0 CB B:THR253 4.4 28.8 1.0 HG22 B:THR293 4.4 41.9 1.0 HA B:VAL287 4.5 36.1 1.0 H B:ASP251 4.5 44.8 1.0 CA B:VAL287 4.5 30.0 1.0 N B:LEU288 4.5 29.3 1.0 N B:THR293 4.5 38.5 1.0 CB B:VAL287 4.6 27.8 1.0 CA B:THR293 4.6 34.0 1.0 N B:GLY292 4.6 35.7 1.0 N B:PRO252 4.6 32.7 1.0 HA B:PRO252 4.6 42.2 1.0 CA B:LEU288 4.7 30.8 1.0 HB2 B:ASP251 4.7 40.8 1.0 CA B:PRO252 4.7 35.1 1.0 CA B:SER290 4.8 41.2 1.0 N B:SER290 4.8 36.1 1.0 CA B:GLY292 4.8 37.1 1.0 OG B:SER290 4.9 43.2 1.0 C B:LEU288 4.9 35.3 1.0 O B:LEU288 4.9 32.6 1.0 N B:ASP251 4.9 37.2 1.0 HA2 B:GLY292 4.9 44.6 1.0 HG1 B:THR253 4.9 37.4 1.0 O B:PRO252 5.0 29.9 1.0 HA3 B:GLY254 5.0 36.6 1.0

R.A.Crespo, Q.Dang, N.E.Zhou, L.M.Guthrie, T.C.Snavely, W.Dong, K.A.Loesch, T.Suzuki, L.You, W.Wang, T.O'malley, T.Parish, D.B.Olsen, J.C.Sacchettini. Structure-Guided Drug Design of 6-Substituted Adenosine Analogues As Potent Inhibitors of Mycobacterium Tuberculosis Adenosine Kinase. J.Med.Chem. V. 62 4483 2019.
ISSN: ISSN 0022-2623
PubMed: 31002508
DOI: 10.1021/ACS.JMEDCHEM.9B00020