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Sodium in PDB 6c9v: Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol

Enzymatic activity of Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol

All present enzymatic activity of Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol:
2.7.1.20;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol, PDB code: 6c9v 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) 43.56 / 1.70
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 50.084, 50.084, 264.752, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol (pdb code 6c9v). 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 (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol, PDB code: 6c9v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6c9v

Go back to Sodium Binding Sites List in 6c9v
Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol


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 (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:25.8
occ:1.00
 O A:ASP251 2.7 17.5 1.0
O A:THR253 2.9 13.4 1.0
O A:VAL287 2.9 17.8 1.0
O A:SER290 2.9 18.6 1.0
HB3 A:ASP251 3.0 26.7 1.0
O A:THR291 3.1 23.4 1.0
HG12 A:VAL287 3.2 17.6 1.0
HG13 A:VAL287 3.2 17.6 1.0
O A:GLY292 3.5 27.7 1.0
C A:ASP251 3.5 19.0 1.0
H A:THR253 3.5 20.5 1.0
CG1 A:VAL287 3.6 14.6 1.0
HB A:THR253 3.6 17.7 1.0
N A:THR253 3.8 17.0 1.0
CB A:ASP251 3.8 22.2 1.0
C A:VAL287 3.8 15.0 1.0
C A:THR253 3.9 14.8 1.0
C A:THR291 3.9 21.1 1.0
C A:SER290 3.9 18.4 1.0
HA A:THR291 3.9 21.1 1.0
OD1 A:ASP251 4.0 18.2 1.0
HA A:THR293 4.0 19.6 1.0
HA A:LEU288 4.1 19.6 1.0
C A:GLY292 4.2 24.9 1.0
CA A:ASP251 4.2 18.3 1.0
CA A:THR253 4.2 17.4 1.0
HG11 A:VAL287 4.2 17.6 1.0
H A:SER290 4.2 22.5 1.0
HG23 A:VAL255 4.3 19.4 1.0
CG A:ASP251 4.3 22.3 1.0
C A:PRO252 4.3 18.4 1.0
H A:ASP251 4.3 21.7 1.0
CA A:THR291 4.3 17.6 1.0
HG22 A:THR293 4.4 20.9 1.0
CB A:THR253 4.4 14.8 1.0
N A:PRO252 4.4 14.9 1.0
HA A:VAL287 4.5 18.2 1.0
N A:THR291 4.5 19.5 1.0
HA A:PRO252 4.6 19.3 1.0
HB2 A:ASP251 4.6 26.7 1.0
N A:ASP251 4.6 18.1 1.0
CA A:VAL287 4.6 15.1 1.0
N A:LEU288 4.7 15.3 1.0
CA A:PRO252 4.7 16.1 1.0
CA A:LEU288 4.7 16.3 1.0
N A:THR293 4.8 17.7 1.0
HG1 A:THR253 4.8 20.7 1.0
CB A:VAL287 4.8 14.6 1.0
N A:GLY292 4.8 26.0 1.0
CA A:THR293 4.8 16.4 1.0
O A:HOH505 4.8 27.1 1.0
N A:SER290 4.9 18.8 1.0
O A:LEU288 4.9 17.6 1.0
O A:PRO252 4.9 15.9 1.0
CA A:SER290 5.0 20.9 1.0
C A:LEU288 5.0 17.6 1.0
CA A:GLY292 5.0 21.8 1.0
OG A:SER290 5.0 26.2 1.0

Sodium binding site 2 out of 2 in 6c9v

Go back to Sodium Binding Sites List in 6c9v
Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol


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 (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(4-Phenylpiperazin-1-Yl)-9H-Purin-9-Yl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:26.5
occ:1.00
 O B:ASP251 2.7 18.6 1.0
O B:VAL287 2.9 18.8 1.0
O B:THR253 2.9 13.9 1.0
O B:SER290 2.9 19.2 1.0
HB3 B:ASP251 3.1 25.9 1.0
HG12 B:VAL287 3.1 18.2 1.0
HG13 B:VAL287 3.1 18.2 1.0
O B:THR291 3.1 24.7 1.0
O B:GLY292 3.5 27.6 1.0
C B:ASP251 3.5 15.4 1.0
CG1 B:VAL287 3.6 15.2 1.0
H B:THR253 3.6 18.6 1.0
HB B:THR253 3.7 17.9 1.0
C B:VAL287 3.8 16.2 1.0
N B:THR253 3.8 15.5 1.0
C B:SER290 3.9 19.2 1.0
CB B:ASP251 3.9 21.6 1.0
C B:THR291 3.9 20.3 1.0
C B:THR253 3.9 14.3 1.0
HA B:THR291 3.9 23.0 1.0
HA B:THR293 4.0 20.1 1.0
OD1 B:ASP251 4.0 18.8 1.0
HA B:LEU288 4.0 18.2 1.0
HG11 B:VAL287 4.1 18.2 1.0
C B:GLY292 4.2 26.6 1.0
CA B:ASP251 4.2 18.3 1.0
H B:SER290 4.2 22.8 1.0
CA B:THR253 4.2 16.7 1.0
HG23 B:VAL255 4.3 19.3 1.0
CG B:ASP251 4.3 19.7 1.0
CA B:THR291 4.3 19.1 1.0
C B:PRO252 4.3 17.0 1.0
H B:ASP251 4.3 22.3 1.0
HG22 B:THR293 4.3 20.7 1.0
CB B:THR253 4.4 14.9 1.0
N B:PRO252 4.4 15.3 1.0
N B:THR291 4.5 20.6 1.0
HA B:VAL287 4.5 18.8 1.0
HA B:PRO252 4.6 19.2 1.0
N B:LEU288 4.6 15.5 1.0
CA B:VAL287 4.6 15.6 1.0
HB2 B:ASP251 4.6 25.9 1.0
N B:ASP251 4.7 18.6 1.0
CA B:PRO252 4.7 16.0 1.0
CA B:LEU288 4.7 15.2 1.0
CB B:VAL287 4.7 14.1 1.0
HG1 B:THR253 4.8 20.3 1.0
N B:THR293 4.8 18.4 1.0
N B:GLY292 4.8 25.3 1.0
CA B:THR293 4.8 16.8 1.0
N B:SER290 4.9 19.0 1.0
O B:HOH513 4.9 25.5 1.0
CA B:SER290 4.9 21.5 1.0
O B:LEU288 4.9 18.1 1.0
C B:LEU288 4.9 17.4 1.0
O B:PRO252 5.0 15.5 1.0
OG B:SER290 5.0 25.6 1.0
CA B:GLY292 5.0 24.4 1.0

Reference:

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
Page generated: Tue Oct 8 06:33:01 2024

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