Sodium in PDB 2ab8: Crystal Structure of T. Gondii Adenosine Kinase Complexed with 6-Methylmercaptopurine Riboside and Amp-Pcp

All present enzymatic activity of Crystal Structure of T. Gondii Adenosine Kinase Complexed with 6-Methylmercaptopurine Riboside and Amp-Pcp:
2.7.1.20;

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with 6-Methylmercaptopurine Riboside and Amp-Pcp, PDB code: 2ab8 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)	45.80 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.489, 61.488, 91.605, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with 6-Methylmercaptopurine Riboside and Amp-Pcp 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 6-Methylmercaptopurine Riboside and Amp-Pcp (pdb code 2ab8). 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 6-Methylmercaptopurine Riboside and Amp-Pcp, PDB code: 2ab8:
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 6-Methylmercaptopurine Riboside and Amp-Pcp


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 6-Methylmercaptopurine Riboside and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2002 b:41.9 occ:1.00 O A:HIS351 2.3 37.2 1.0 O A:GLY353 2.3 39.1 1.0 O A:VAL348 2.4 34.2 1.0 O A:HOH2234 2.4 58.9 1.0 O A:HOH2235 2.7 49.0 1.0 C A:GLY353 3.4 43.4 1.0 C A:VAL348 3.5 30.6 1.0 C A:HIS351 3.5 43.0 1.0 N A:GLY353 3.5 42.7 1.0 CG1 A:VAL348 3.8 32.8 1.0 C A:VAL352 4.0 43.3 1.0 CA A:GLY353 4.0 43.3 1.0 CA A:VAL352 4.2 45.4 1.0 CA A:ILE349 4.2 30.2 1.0 O A:ASP312 4.3 39.6 1.0 N A:ILE349 4.3 27.4 1.0 N A:VAL352 4.3 44.8 1.0 N A:HIS351 4.3 35.8 1.0 CD2 A:PHE354 4.4 51.0 1.0 CA A:VAL348 4.4 30.5 1.0 N A:PHE354 4.5 39.8 1.0 CA A:HIS351 4.5 42.2 1.0 O A:ASN314 4.5 37.5 1.0 C A:ILE349 4.6 35.2 1.0 CA A:PHE354 4.7 41.6 1.0 CB A:ASP312 4.7 51.7 1.0 CB A:VAL348 4.8 33.5 1.0 CE2 A:PHE354 4.8 55.5 1.0 O A:VAL352 4.8 45.8 1.0 CG A:HIS351 4.9 44.6 1.0 N A:GLN350 4.9 33.0 1.0 O A:ILE349 5.0 34.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of T. Gondii Adenosine Kinase Complexed with 6-Methylmercaptopurine Riboside and Amp-Pcp


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 6-Methylmercaptopurine Riboside and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2003 b:27.2 occ:1.00 O A:HOH2100 2.3 31.6 1.0 OD1 A:ASN268 2.4 22.2 1.0 O A:THR269 2.4 22.7 1.0 O A:THR290 2.5 18.1 1.0 O A:HOH2101 2.5 45.6 1.0 O A:ALA291 3.3 20.4 1.0 CG A:ASN268 3.3 20.8 1.0 C A:THR290 3.4 19.8 1.0 C A:THR269 3.6 21.5 1.0 CA A:ALA291 3.7 20.9 1.0 C A:ALA291 3.7 19.3 1.0 ND2 A:ASN268 3.8 22.9 1.0 NE2 A:GLN289 3.8 17.1 1.0 N A:ALA291 3.9 18.9 1.0 N A:THR269 3.9 20.9 1.0 O A:GLN289 3.9 20.1 1.0 O A:ALA271 4.1 21.9 1.0 CG A:GLN289 4.1 18.4 1.0 CD A:GLN289 4.2 21.1 1.0 N A:GLY293 4.3 17.2 1.0 C A:GLN289 4.4 23.1 1.0 CA A:THR269 4.4 20.6 1.0 CA A:THR290 4.5 17.8 1.0 CB A:ASN268 4.6 21.1 1.0 N A:SER270 4.6 19.5 1.0 CA A:SER270 4.6 15.6 1.0 C A:ASN268 4.6 21.6 1.0 N A:ASP292 4.6 20.7 1.0 N A:THR290 4.7 16.2 1.0 CA A:ASN268 4.7 21.9 1.0 CA A:GLY293 4.7 15.1 1.0 C A:SER270 4.8 21.2 1.0 CB A:GLN289 4.9 20.8 1.0 N A:ALA271 5.0 18.7 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