Sodium in PDB 2a9z: Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine and Amp-Pcp

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

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine and Amp-Pcp, PDB code: 2a9z 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 (°)	60.068, 61.588, 91.650, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 19.6

The structure of Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine 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 N6- Dimethyladenosine and Amp-Pcp (pdb code 2a9z). 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 and Amp-Pcp, PDB code: 2a9z:
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 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 N6- Dimethyladenosine and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2002 b:19.4 occ:1.00 O A:HOH5102 2.0 39.8 1.0 O A:HOH5161 2.2 24.0 1.0 OD1 A:ASN268 2.3 14.3 1.0 O A:THR269 2.4 16.4 1.0 O A:THR290 2.5 14.1 1.0 O A:ALA291 3.3 14.9 1.0 CG A:ASN268 3.4 13.4 1.0 C A:THR290 3.4 14.7 1.0 C A:THR269 3.6 13.4 1.0 C A:ALA291 3.6 16.5 1.0 CA A:ALA291 3.6 15.1 1.0 O A:HOH5099 3.7 33.1 1.0 OE1 A:GLN289 3.7 22.7 1.0 ND2 A:ASN268 3.8 14.2 1.0 N A:ALA291 3.9 14.7 1.0 N A:THR269 3.9 11.9 1.0 O A:GLN289 4.0 17.3 1.0 CD A:GLN289 4.1 14.0 1.0 O A:ALA271 4.2 17.1 1.0 CG A:GLN289 4.2 15.1 1.0 N A:GLY293 4.3 15.7 1.0 C A:GLN289 4.4 14.2 1.0 CA A:THR269 4.5 14.0 1.0 N A:SER270 4.6 14.7 1.0 C A:ASN268 4.6 13.1 1.0 CA A:THR290 4.6 13.9 1.0 N A:ASP292 4.6 15.4 1.0 CA A:SER270 4.6 15.2 1.0 CB A:ASN268 4.6 12.9 1.0 CA A:ASN268 4.6 13.2 1.0 O A:HOH5237 4.7 44.0 1.0 N A:THR290 4.7 12.9 1.0 CA A:GLY293 4.8 13.9 1.0 C A:SER270 4.8 17.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of T. Gondii Adenosine Kinase Complexed with N6- Dimethyladenosine 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 N6- Dimethyladenosine and Amp-Pcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2003 b:21.9 occ:1.00 O A:HIS351 2.2 21.9 1.0 O A:GLY353 2.2 20.5 1.0 O A:VAL348 2.3 18.0 1.0 O A:HOH5168 2.4 27.1 1.0 O A:HOH5209 2.7 37.5 1.0 C A:GLY353 3.3 20.0 1.0 N A:GLY353 3.3 26.0 1.0 C A:HIS351 3.4 22.7 1.0 C A:VAL348 3.5 17.6 1.0 C A:VAL352 3.6 26.6 1.0 CG1 A:VAL348 3.8 19.0 1.0 CA A:GLY353 3.9 25.7 1.0 CA A:VAL352 4.0 26.1 1.0 O A:VAL352 4.1 27.7 1.0 N A:VAL352 4.2 26.7 1.0 CA A:ILE349 4.3 16.1 1.0 N A:HIS351 4.3 19.9 1.0 N A:ILE349 4.3 15.7 1.0 CA A:VAL348 4.4 15.7 1.0 O A:ASP312 4.4 23.1 1.0 CD2 A:HIS351 4.4 23.9 1.0 N A:PHE354 4.4 17.1 1.0 CA A:HIS351 4.5 20.0 1.0 C A:ILE349 4.6 19.8 1.0 CD2 A:PHE354 4.6 20.2 1.0 CB A:VAL348 4.7 17.5 1.0 NE2 A:HIS351 4.7 26.7 1.0 CA A:PHE354 4.8 16.8 1.0 O A:ASN314 4.8 21.4 1.0 CG A:HIS351 4.8 22.1 1.0 OD1 A:ASP312 4.9 36.1 1.0 O A:ILE349 4.9 20.6 1.0 N A:GLN350 4.9 16.8 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