Sodium in PDB 6c9p: Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside

All present enzymatic activity of Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside:
2.7.1.20;

The structure of Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside, PDB code: 6c9p 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)	34.96 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	49.438, 49.438, 263.986, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 23.5

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside (pdb code 6c9p). 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 6- Methylmercaptopurine Riboside, PDB code: 6c9p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside


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 6- Methylmercaptopurine Riboside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:49.5 occ:1.00 O A:ASP251 2.7 40.3 1.0 O A:SER290 2.8 38.8 1.0 HB3 A:ASP251 2.8 56.5 1.0 O A:THR253 2.9 38.7 1.0 O A:VAL287 2.9 36.4 1.0 O A:THR291 3.0 46.9 1.0 HG13 A:VAL287 3.2 53.0 1.0 O A:GLY292 3.2 44.2 1.0 HG12 A:VAL287 3.4 53.0 1.0 C A:ASP251 3.5 40.7 1.0 H A:THR253 3.6 45.0 1.0 CB A:ASP251 3.6 47.0 1.0 HB A:THR253 3.7 46.4 1.0 CG1 A:VAL287 3.7 44.1 1.0 C A:THR291 3.8 49.4 1.0 N A:THR253 3.8 37.5 1.0 OD1 A:ASP251 3.8 43.5 1.0 C A:SER290 3.8 45.0 1.0 C A:VAL287 3.9 39.0 1.0 C A:THR253 3.9 40.7 1.0 HA A:LEU288 3.9 44.7 1.0 CG A:ASP251 4.0 47.5 1.0 HA A:THR293 4.0 46.8 1.0 C A:GLY292 4.0 50.5 1.0 HA A:THR291 4.1 63.2 1.0 CA A:ASP251 4.1 45.7 1.0 H A:SER290 4.2 50.9 1.0 CA A:THR253 4.2 44.1 1.0 C A:PRO252 4.3 44.9 1.0 HG11 A:VAL287 4.3 53.0 1.0 HG23 A:VAL255 4.3 41.9 1.0 CA A:THR291 4.3 52.6 1.0 HB2 A:ASP251 4.3 56.5 1.0 N A:PRO252 4.4 41.3 1.0 H A:ASP251 4.4 51.7 1.0 CB A:THR253 4.4 38.6 1.0 N A:THR291 4.5 48.5 1.0 HG22 A:THR293 4.5 46.8 1.0 CA A:LEU288 4.6 37.2 1.0 N A:LEU288 4.6 36.9 1.0 HA A:PRO252 4.6 50.5 1.0 N A:GLY292 4.6 48.2 1.0 CA A:PRO252 4.6 42.1 1.0 N A:ASP251 4.7 43.0 1.0 HG23 A:THR250 4.7 63.4 1.0 HA A:VAL287 4.7 45.4 1.0 HG1 A:THR253 4.7 51.0 1.0 CA A:VAL287 4.7 37.8 1.0 O A:LEU288 4.8 39.4 1.0 N A:THR293 4.8 41.6 1.0 C A:LEU288 4.8 39.5 1.0 N A:SER290 4.8 42.4 1.0 OG A:SER290 4.8 47.4 1.0 CA A:GLY292 4.8 51.0 1.0 CA A:THR293 4.8 38.9 1.0 CA A:SER290 4.9 46.0 1.0 HG22 A:VAL255 4.9 41.9 1.0 CB A:VAL287 4.9 37.2 1.0 HA A:ASP251 5.0 54.9 1.0 O A:PRO252 5.0 37.0 1.0

Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to 6- Methylmercaptopurine Riboside


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 6- Methylmercaptopurine Riboside within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:46.2 occ:1.00 O B:ASP251 2.6 40.5 1.0 HB3 B:ASP251 2.7 58.3 1.0 O B:SER290 2.8 42.4 1.0 O B:THR253 2.9 35.9 1.0 O B:VAL287 3.0 37.6 1.0 O B:THR291 3.0 48.5 1.0 O B:GLY292 3.2 48.2 1.0 HG13 B:VAL287 3.3 54.0 1.0 HG12 B:VAL287 3.4 54.0 1.0 C B:ASP251 3.4 36.1 1.0 H B:THR253 3.5 43.1 1.0 CB B:ASP251 3.6 48.5 1.0 HB B:THR253 3.6 45.8 1.0 N B:THR253 3.7 35.8 1.0 OD1 B:ASP251 3.7 41.9 1.0 C B:THR291 3.8 51.9 1.0 CG1 B:VAL287 3.8 45.0 1.0 C B:THR253 3.8 36.3 1.0 C B:SER290 3.9 46.2 1.0 C B:VAL287 3.9 37.8 1.0 HA B:LEU288 4.0 45.6 1.0 CG B:ASP251 4.0 46.5 1.0 HA B:THR291 4.1 62.9 1.0 HA B:THR293 4.1 47.2 1.0 CA B:ASP251 4.1 44.9 1.0 C B:GLY292 4.1 50.9 1.0 CA B:THR253 4.2 42.7 1.0 C B:PRO252 4.2 40.5 1.0 HG23 B:VAL255 4.3 43.3 1.0 H B:SER290 4.3 51.5 1.0 N B:PRO252 4.3 37.2 1.0 HB2 B:ASP251 4.3 58.3 1.0 CB B:THR253 4.3 38.1 1.0 CA B:THR291 4.4 52.4 1.0 H B:ASP251 4.4 51.0 1.0 HG11 B:VAL287 4.4 54.0 1.0 HG22 B:THR293 4.5 47.2 1.0 N B:THR291 4.5 51.8 1.0 HA B:PRO252 4.5 43.3 1.0 CA B:PRO252 4.6 36.0 1.0 CA B:LEU288 4.6 38.0 1.0 HG1 B:THR253 4.6 47.6 1.0 N B:LEU288 4.7 37.5 1.0 N B:GLY292 4.7 48.8 1.0 N B:ASP251 4.7 42.5 1.0 HG23 B:THR250 4.7 67.2 1.0 HA B:VAL287 4.8 44.0 1.0 O B:LEU288 4.8 39.5 1.0 N B:THR293 4.8 44.7 1.0 HG22 B:VAL255 4.8 43.3 1.0 CA B:VAL287 4.8 36.6 1.0 C B:LEU288 4.9 42.0 1.0 CA B:GLY292 4.9 50.2 1.0 CA B:THR293 4.9 39.3 1.0 O B:PRO252 4.9 35.5 1.0 HA B:ASP251 4.9 53.9 1.0 N B:SER290 4.9 42.8 1.0 CA B:SER290 4.9 47.2 1.0 OG B:SER290 4.9 51.0 1.0 CB B:VAL287 5.0 35.9 1.0 CG2 B:VAL255 5.0 36.1 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