Sodium in PDB 2a9y: Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine

All present enzymatic activity of Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine:
2.7.1.20;

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine, PDB code: 2a9y was solved by Y.Zhang, M.H.El Kouni, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.285, 61.516, 91.828, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 19.6

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine (pdb code 2a9y). 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 T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine, PDB code: 2a9y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine


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 T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2002 b:19.5 occ:1.00 O A:HOH6381 2.2 23.0 1.0 OD1 A:ASN268 2.3 13.4 1.0 O A:THR269 2.4 15.8 1.0 O A:THR290 2.5 13.1 1.0 O A:HOH6387 3.2 36.5 1.0 CG A:ASN268 3.3 12.6 1.0 O A:ALA291 3.3 14.5 1.0 C A:THR290 3.4 13.2 1.0 CA A:ALA291 3.6 15.1 1.0 C A:THR269 3.6 14.4 1.0 NE2 A:GLN289 3.6 23.6 1.0 C A:ALA291 3.6 15.6 1.0 ND2 A:ASN268 3.8 13.8 1.0 N A:ALA291 3.9 15.8 1.0 N A:THR269 4.0 14.2 1.0 O A:GLN289 4.1 18.0 1.0 CD A:GLN289 4.1 16.9 1.0 O A:ALA271 4.2 17.4 1.0 CG A:GLN289 4.2 15.3 1.0 N A:GLY293 4.3 14.5 1.0 CA A:THR269 4.5 14.4 1.0 C A:GLN289 4.5 12.7 1.0 CB A:ASN268 4.6 14.7 1.0 C A:ASN268 4.6 13.9 1.0 N A:ASP292 4.6 13.5 1.0 CA A:THR290 4.6 13.7 1.0 N A:SER270 4.6 16.0 1.0 CA A:SER270 4.6 15.4 1.0 CA A:ASN268 4.6 13.3 1.0 N A:THR290 4.7 12.6 1.0 CA A:GLY293 4.8 13.1 1.0 C A:SER270 4.8 16.7 1.0 OE1 A:GLN289 5.0 23.8 1.0 CB A:GLN289 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine


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 T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2003 b:18.9 occ:1.00 O A:HOH6105 2.3 24.4 1.0 O A:HIS351 2.3 19.4 1.0 O A:GLY353 2.3 19.1 1.0 O A:VAL348 2.3 15.6 1.0 O A:HOH6144 2.6 32.9 1.0 C A:GLY353 3.4 18.3 1.0 C A:VAL348 3.5 14.5 1.0 C A:HIS351 3.5 20.9 1.0 N A:GLY353 3.5 23.3 1.0 C A:VAL352 3.7 23.9 1.0 CG1 A:VAL348 3.8 18.5 1.0 CA A:VAL352 4.0 22.7 1.0 CA A:GLY353 4.0 23.1 1.0 O A:VAL352 4.1 23.8 1.0 CA A:ILE349 4.2 14.8 1.0 N A:VAL352 4.2 25.7 1.0 N A:ILE349 4.3 14.5 1.0 O A:ASP312 4.3 19.2 1.0 N A:HIS351 4.3 19.3 1.0 CA A:VAL348 4.4 14.7 1.0 CD2 A:HIS351 4.4 23.0 1.0 N A:PHE354 4.5 15.5 1.0 CA A:HIS351 4.5 21.0 1.0 CD2 A:PHE354 4.5 17.9 1.0 C A:ILE349 4.5 16.4 1.0 CB A:VAL348 4.7 15.4 1.0 O A:ASN314 4.7 19.3 1.0 NE2 A:HIS351 4.8 24.9 1.0 CA A:PHE354 4.8 16.3 1.0 O A:ILE349 4.8 17.2 1.0 CG A:HIS351 4.9 22.2 1.0 CB A:ASP312 4.9 27.6 1.0 CE2 A:PHE354 4.9 20.5 1.0 N A:GLN350 4.9 15.0 1.0 OD1 A:ASP312 5.0 29.0 1.0

Y.Zhang, M.H.El Kouni, S.E.Ealick. Substrate Analogs Induce An Intermediate Conformational Change in Toxoplasma Gondii Adenosine Kinase Acta Crystallogr.,Sect.D V. 63 126 2007.
ISSN: ISSN 0907-4449
PubMed: 17242506
DOI: 10.1107/S0907444906043654