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Sodium in PDB 6c9r: Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(Thiophen-3-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-(Thiophen-3-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-(Thiophen-3-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-(Thiophen-3-Yl)-9H-Purin-9-Yl)Tetrahydrofuran-3, 4-Diol, PDB code: 6c9r 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) 44.38 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.236, 81.984, 158.330, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.4

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-(Thiophen-3-Yl)-9H-Purin-9-Yl)Tetrahydrofuran-3, 4-Diol (pdb code 6c9r). 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-(Thiophen-3-Yl)-9H-Purin-9-Yl)Tetrahydrofuran-3, 4-Diol, PDB code: 6c9r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6c9r

Go back to Sodium Binding Sites List in 6c9r
Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(Thiophen-3-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-(Thiophen-3-Yl)-9H-Purin-9-Yl)Tetrahydrofuran-3, 4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:34.9
occ:1.00
 O A:VAL287 2.4 27.9 1.0
O A:SER290 2.4 35.7 1.0
O A:GLY292 2.6 31.5 1.0
HG13 A:VAL287 2.8 33.5 1.0
HB3 A:ASP251 3.0 52.3 1.0
O A:ASP251 3.0 37.5 1.0
HG12 A:VAL287 3.2 33.5 1.0
C A:VAL287 3.4 30.6 1.0
CG1 A:VAL287 3.5 27.9 1.0
C A:SER290 3.5 36.7 1.0
C A:GLY292 3.6 30.7 1.0
H A:SER290 3.6 44.0 1.0
H A:GLY292 3.7 41.5 1.0
OD2 A:ASP251 3.7 54.6 1.0
O A:THR253 3.7 28.3 1.0
CB A:ASP251 3.8 43.5 1.0
N A:GLY292 3.9 34.5 1.0
HA A:THR293 4.0 35.6 1.0
HA A:VAL287 4.0 32.5 1.0
C A:ASP251 4.0 39.2 1.0
HA A:THR291 4.0 52.0 1.0
CG A:ASP251 4.0 47.2 1.0
HA A:LEU288 4.0 34.8 1.0
OG A:SER290 4.1 36.4 1.0
HG11 A:VAL287 4.1 33.5 1.0
CA A:VAL287 4.2 27.1 1.0
O A:HOH526 4.2 35.5 1.0
HG A:SER290 4.3 43.7 1.0
N A:SER290 4.3 36.5 1.0
C A:THR291 4.3 36.3 1.0
CA A:GLY292 4.3 36.0 1.0
CA A:ASP251 4.4 38.7 1.0
N A:LEU288 4.4 31.2 1.0
CA A:SER290 4.4 39.0 1.0
N A:THR291 4.4 37.5 1.0
CA A:THR291 4.4 43.3 1.0
H A:ASP251 4.4 43.6 1.0
CB A:VAL287 4.5 26.0 1.0
H A:THR253 4.5 38.6 1.0
CA A:LEU288 4.5 28.9 1.0
N A:THR293 4.5 30.9 1.0
HB2 A:ASP251 4.5 52.3 1.0
C A:LEU288 4.6 32.3 1.0
O A:LEU288 4.6 30.2 1.0
HB A:THR253 4.6 41.2 1.0
N A:ASP251 4.7 36.2 1.0
CA A:THR293 4.7 29.6 1.0
HA2 A:GLY292 4.7 43.3 1.0
N A:THR253 4.8 32.1 1.0
CB A:SER290 4.8 40.2 1.0
C A:THR253 4.8 29.0 1.0
HG23 A:VAL255 4.8 29.2 1.0
HG22 A:THR293 4.8 35.2 1.0
OD1 A:ASP251 4.9 44.4 1.0

Sodium binding site 2 out of 2 in 6c9r

Go back to Sodium Binding Sites List in 6c9r
Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3S,4R,5R)-2- (Hydroxymethyl)-5-(6-(Thiophen-3-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-(Thiophen-3-Yl)-9H-Purin-9-Yl)Tetrahydrofuran-3, 4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:34.7
occ:1.00
 O B:SER290 2.4 36.6 1.0
O B:VAL287 2.5 30.4 1.0
O B:ASP251 2.7 41.8 1.0
O B:GLY292 2.7 36.2 1.0
HB3 B:ASP251 2.8 52.1 1.0
HG13 B:VAL287 3.0 36.5 1.0
HG12 B:VAL287 3.2 36.5 1.0
OD2 B:ASP251 3.2 46.1 1.0
O B:THR253 3.3 33.4 1.0
CB B:ASP251 3.5 43.4 1.0
C B:VAL287 3.5 30.7 1.0
CG1 B:VAL287 3.5 30.4 1.0
C B:SER290 3.6 36.2 1.0
CG B:ASP251 3.6 46.2 1.0
C B:ASP251 3.7 42.3 1.0
H B:GLY292 3.7 44.1 1.0
C B:GLY292 3.7 32.1 1.0
H B:SER290 3.8 43.1 1.0
HA B:THR291 3.9 45.6 1.0
N B:GLY292 3.9 36.7 1.0
HA B:LEU288 3.9 38.8 1.0
HA B:THR293 4.0 37.4 1.0
H B:THR253 4.0 45.1 1.0
CA B:ASP251 4.1 46.6 1.0
HB B:THR253 4.1 50.3 1.0
HG11 B:VAL287 4.2 36.5 1.0
HA B:VAL287 4.2 34.0 1.0
HB2 B:ASP251 4.3 52.1 1.0
C B:THR291 4.3 38.7 1.0
N B:THR253 4.3 37.5 1.0
OG B:SER290 4.3 37.1 1.0
C B:THR253 4.3 32.2 1.0
CA B:VAL287 4.3 28.2 1.0
CA B:THR291 4.4 38.0 1.0
H B:ASP251 4.4 55.5 1.0
CA B:GLY292 4.4 34.9 1.0
O B:HOH529 4.4 36.7 1.0
N B:LEU288 4.4 32.0 1.0
N B:THR291 4.4 40.4 1.0
HG B:SER290 4.4 44.6 1.0
N B:SER290 4.4 35.9 1.0
CA B:LEU288 4.5 32.2 1.0
CA B:SER290 4.5 36.6 1.0
OD1 B:ASP251 4.5 46.3 1.0
O B:LEU288 4.6 36.5 1.0
CB B:VAL287 4.6 28.4 1.0
C B:LEU288 4.6 36.4 1.0
N B:ASP251 4.6 46.1 1.0
N B:THR293 4.6 34.1 1.0
HG23 B:VAL255 4.7 41.5 1.0
N B:PRO252 4.7 38.5 1.0
CA B:THR253 4.8 39.5 1.0
CA B:THR293 4.8 31.1 1.0
HG22 B:THR293 4.8 38.2 1.0
HA2 B:GLY292 4.8 42.0 1.0
C B:PRO252 4.8 35.4 1.0
CB B:THR253 4.9 41.8 1.0
HA B:PRO252 5.0 41.5 1.0
CB B:SER290 5.0 37.7 1.0
HA B:ASP251 5.0 56.0 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 06:32:30 2024

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