Atomistry » Sodium » PDB 6c12-6chk » 6c9r
Atomistry »
  Sodium »
    PDB 6c12-6chk »
      6c9r »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy