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Sodium in PDB 6c9s: Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol

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

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

Protein crystallography data

The structure of Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol, PDB code: 6c9s 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) 35.29 / 2.23
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 49.910, 49.910, 264.377, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol (pdb code 6c9s). 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,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol, PDB code: 6c9s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6c9s

Go back to Sodium Binding Sites List in 6c9s
Sodium binding site 1 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) 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,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:42.4
occ:1.00
 O A:ASP251 2.7 30.1 1.0
O A:VAL287 2.9 34.7 1.0
O A:THR253 2.9 32.5 1.0
O A:SER290 2.9 35.2 1.0
HG13 A:VAL287 2.9 39.2 1.0
HB3 A:ASP251 3.0 43.8 1.0
O A:GLY292 3.2 47.4 1.0
HG12 A:VAL287 3.3 39.2 1.0
C A:ASP251 3.5 34.2 1.0
CG1 A:VAL287 3.6 32.5 1.0
OD1 A:ASP251 3.6 40.8 1.0
H A:GLY292 3.6 42.4 1.0
H A:THR253 3.7 41.5 1.0
HB A:THR253 3.7 42.5 1.0
CB A:ASP251 3.8 36.3 1.0
C A:VAL287 3.8 33.0 1.0
N A:THR253 3.9 34.4 1.0
C A:GLY292 3.9 45.5 1.0
C A:THR253 3.9 33.6 1.0
HA A:THR291 3.9 51.9 1.0
N A:GLY292 4.0 35.2 1.0
HA A:LEU288 4.0 35.2 1.0
C A:SER290 4.0 41.1 1.0
HG11 A:VAL287 4.1 39.2 1.0
CG A:ASP251 4.1 39.7 1.0
HA A:THR293 4.1 42.4 1.0
CA A:ASP251 4.2 35.9 1.0
H A:SER290 4.3 44.3 1.0
HG23 A:VAL255 4.3 34.8 1.0
CA A:THR253 4.3 33.8 1.0
C A:PRO252 4.3 35.9 1.0
H A:ASP251 4.3 45.4 1.0
N A:PRO252 4.5 33.8 1.0
CB A:THR253 4.5 35.2 1.0
CA A:GLY292 4.5 43.8 1.0
CA A:THR291 4.6 43.0 1.0
HB2 A:ASP251 4.6 43.8 1.0
C A:THR291 4.6 45.2 1.0
HA A:VAL287 4.6 39.3 1.0
HG22 A:THR293 4.6 40.3 1.0
N A:LEU288 4.6 30.1 1.0
HA A:PRO252 4.6 40.9 1.0
N A:ASP251 4.6 37.6 1.0
O A:HOH505 4.7 43.2 1.0
CA A:VAL287 4.7 32.6 1.0
CA A:LEU288 4.7 29.2 1.0
CA A:PRO252 4.7 33.9 1.0
N A:THR293 4.7 40.4 1.0
CB A:VAL287 4.7 33.8 1.0
N A:THR291 4.8 49.8 1.0
HA2 A:GLY292 4.8 52.8 1.0
OG A:SER290 4.9 41.2 1.0
HG1 A:THR253 4.9 37.5 1.0
CA A:THR293 4.9 35.1 1.0
HG A:SER290 4.9 49.7 1.0
O A:PRO252 4.9 32.1 1.0
C A:LEU288 4.9 34.2 1.0
O A:LEU288 5.0 30.6 1.0
N A:SER290 5.0 36.8 1.0

Sodium binding site 2 out of 2 in 6c9s

Go back to Sodium Binding Sites List in 6c9s
Sodium binding site 2 out of 2 in the Mycobacterium Tuberculosis Adenosine Kinase Bound to (2R,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) 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,3R,4S,5R)-2- (6-([1,1'-Biphenyl]-4-Ylethynyl)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:43.4
occ:1.00
 O B:ASP251 2.7 31.6 1.0
O B:VAL287 2.8 33.9 1.0
O B:SER290 2.9 34.5 1.0
HB3 B:ASP251 2.9 46.7 1.0
O B:THR253 2.9 31.9 1.0
HG13 B:VAL287 3.0 38.0 1.0
O B:GLY292 3.2 47.7 1.0
HG12 B:VAL287 3.4 38.0 1.0
OD1 B:ASP251 3.5 41.8 1.0
C B:ASP251 3.5 33.4 1.0
H B:GLY292 3.6 40.3 1.0
CG1 B:VAL287 3.6 31.5 1.0
CB B:ASP251 3.7 38.8 1.0
H B:THR253 3.7 40.5 1.0
HB B:THR253 3.7 45.0 1.0
C B:VAL287 3.9 32.3 1.0
C B:GLY292 3.9 43.3 1.0
N B:THR253 3.9 33.6 1.0
HA B:THR291 3.9 49.4 1.0
C B:THR253 4.0 34.2 1.0
N B:GLY292 4.0 33.4 1.0
CG B:ASP251 4.0 40.4 1.0
C B:SER290 4.0 38.2 1.0
HA B:LEU288 4.1 35.4 1.0
HA B:THR293 4.1 40.5 1.0
HG11 B:VAL287 4.1 38.0 1.0
CA B:ASP251 4.1 36.7 1.0
H B:SER290 4.3 43.9 1.0
HG23 B:VAL255 4.3 32.9 1.0
CA B:THR253 4.3 33.5 1.0
H B:ASP251 4.3 43.9 1.0
C B:PRO252 4.4 36.1 1.0
N B:PRO252 4.5 34.7 1.0
CB B:THR253 4.5 37.4 1.0
CA B:GLY292 4.5 43.1 1.0
HB2 B:ASP251 4.5 46.7 1.0
CA B:THR291 4.5 41.0 1.0
C B:THR291 4.5 41.6 1.0
HA B:VAL287 4.6 38.8 1.0
HG22 B:THR293 4.6 39.7 1.0
N B:ASP251 4.6 36.4 1.0
N B:LEU288 4.7 28.6 1.0
CA B:VAL287 4.7 32.1 1.0
HA B:PRO252 4.7 38.4 1.0
CA B:LEU288 4.7 29.3 1.0
N B:THR293 4.7 39.6 1.0
N B:THR291 4.7 43.5 1.0
CA B:PRO252 4.7 31.9 1.0
CB B:VAL287 4.8 32.6 1.0
HA2 B:GLY292 4.8 51.9 1.0
CA B:THR293 4.9 33.6 1.0
HG1 B:THR253 4.9 37.8 1.0
OG B:SER290 4.9 41.6 1.0
HG B:SER290 4.9 50.1 1.0
C B:LEU288 4.9 35.2 1.0
N B:SER290 5.0 36.4 1.0
O B:PRO252 5.0 33.0 1.0
O B:LEU288 5.0 30.3 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 06:32:44 2024

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