Sodium in PDB 3otx: Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A:
2.7.1.20;

The structure of Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A, PDB code: 3otx was solved by S.Kuettel, J.Greenwald, D.Kostrewa, S.Ahmed, L.Scapozza, R.Perozzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.36 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.893, 70.549, 72.410, 90.00, 90.77, 90.00
R / Rfree (%)	18.1 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A (pdb code 3otx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A, PDB code: 3otx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na347 b:25.3 occ:1.00 O A:HOH639 2.3 18.8 1.0 O1E A:AP5346 2.4 20.1 1.0 O A:HOH472 2.4 17.5 1.0 O A:HOH384 2.5 17.7 1.0 O A:HOH638 2.6 18.1 1.0 O2D A:AP5346 2.6 20.8 1.0 PE A:AP5346 3.4 18.9 1.0 O5J A:AP5346 3.5 19.1 1.0 PD A:AP5346 3.6 19.9 1.0 O A:HOH636 3.6 25.4 1.0 OD1 A:ASP299 3.7 16.5 1.0 O3G A:AP5346 3.7 20.0 1.0 O A:HOH456 3.7 18.4 1.0 O3D A:AP5346 3.9 16.4 1.0 O A:HOH371 4.0 18.2 1.0 O A:HOH637 4.0 39.8 1.0 N A:ASP299 4.2 14.5 1.0 CA A:GLY298 4.2 14.3 1.0 CG A:ASP299 4.2 14.6 1.0 O2B A:AP5346 4.3 16.0 1.0 C A:GLY298 4.5 14.4 1.0 OD2 A:ASP299 4.5 13.9 1.0 O A:SER197 4.7 16.8 1.0 N A:GLY298 4.7 13.5 1.0 OD1 A:ASN195 4.8 22.1 0.5 OG A:SER64 4.8 18.6 1.0 C5J A:AP5346 4.8 18.0 1.0 O2E A:AP5346 4.8 21.1 1.0 O A:HOH373 4.9 32.2 1.0 ND2 A:ASN195 4.9 25.7 0.5 O A:HOH496 5.0 30.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Trypanosoma Brucei Rhodesiense Adenosine Kinase Complexed with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na347 b:28.8 occ:1.00 O B:HOH632 2.3 22.6 1.0 O B:HOH631 2.4 25.5 1.0 O B:HOH417 2.4 25.4 1.0 O B:HOH630 2.4 20.4 1.0 O1E B:AP5346 2.5 21.6 1.0 O2D B:AP5346 2.7 19.8 1.0 O5J B:AP5346 3.3 20.5 1.0 PE B:AP5346 3.4 19.6 1.0 OD1 B:ASP299 3.5 17.0 1.0 O B:HOH448 3.7 18.2 1.0 PD B:AP5346 3.7 18.9 1.0 O B:HOH402 3.9 26.2 1.0 O3G B:AP5346 3.9 15.1 1.0 O3D B:AP5346 3.9 14.9 1.0 O B:HOH415 4.2 21.7 1.0 CG B:ASP299 4.2 17.3 1.0 N B:ASP299 4.2 13.3 1.0 CA B:GLY298 4.3 13.9 1.0 O2B B:AP5346 4.3 14.3 1.0 OD2 B:ASP299 4.5 17.7 1.0 C B:GLY298 4.6 15.3 1.0 OG B:SER64 4.6 20.0 1.0 O B:SER197 4.7 19.3 1.0 C5J B:AP5346 4.7 14.1 1.0 O2E B:AP5346 4.8 19.2 1.0 ND2 B:ASN195 4.8 21.3 0.5 N B:GLY298 4.8 14.7 1.0 O B:HOH587 4.9 31.0 1.0

S.Kuettel, J.Greenwald, D.Kostrewa, S.Ahmed, L.Scapozza, R.Perozzo. Crystal Structures of T. B. Rhodesiense Adenosine Kinase Complexed with Inhibitor and Activator: Implications For Catalysis and Hyperactivation Plos Negl Trop Dis V. 5 E1164 2011.
ISSN: ISSN 1935-2727
PubMed: 21629723
DOI: 10.1371/JOURNAL.PNTD.0001164