Sodium in PDB 2zs9: Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate

All present enzymatic activity of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate:
2.7.1.33;

The structure of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate, PDB code: 2zs9 was solved by B.Chetnani, S.Das, P.Kumar, A.Surolia, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.12 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.194, 104.194, 90.304, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 23.3

The binding sites of Sodium atom in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate (pdb code 2zs9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate, PDB code: 2zs9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na708 b:72.1 occ:1.00 CB A:SER303 3.0 47.4 1.0 OE2 A:GLU48 3.2 64.3 1.0 CA A:SER303 3.6 40.1 1.0 CD A:GLU48 3.6 64.3 1.0 OE1 A:GLU48 3.8 64.3 1.0 OG A:SER303 4.2 47.4 1.0 NH2 A:ARG15 4.2 66.3 1.0 N A:SER303 4.3 40.1 1.0 CB A:GLU48 4.4 64.3 1.0 CB A:GLN43 4.5 78.1 1.0 CG A:GLU48 4.5 64.3 1.0 C A:SER303 4.8 40.1 1.0 N A:ILE44 4.9 54.4 1.0 OD1 A:ASP45 4.9 58.8 1.0 C A:GLN43 4.9 74.4 1.0 C A:HIS302 4.9 52.5 1.0 OD2 A:ASP45 4.9 58.8 1.0 CA A:ILE44 4.9 54.4 1.0 O A:HIS302 5.0 52.5 1.0

Sodium binding site 2 out of 3 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na709 b:60.5 occ:1.00 O A:HOH401 2.8 45.4 1.0 O A:HOH404 2.8 40.6 1.0 O A:THR127 3.2 39.1 1.0 O A:PRO175 3.4 29.5 1.0 OE1 A:GLN190 3.7 37.8 1.0 OG1 A:THR127 3.7 36.0 1.0 N A:GLY130 3.8 48.0 1.0 CA A:GLY130 3.8 48.0 1.0 CG1 A:VAL126 4.1 30.0 1.0 N A:THR127 4.2 39.1 1.0 C A:THR127 4.2 39.1 1.0 C A:PRO175 4.5 29.5 1.0 CA A:VAL176 4.6 34.3 1.0 CA A:THR127 4.7 39.1 1.0 CB A:THR127 4.8 36.0 1.0 C A:GLY130 4.8 48.0 1.0 CD A:GLN190 4.9 37.8 1.0 CB A:ALA174 4.9 35.7 1.0 N A:TYR177 4.9 43.1 1.0 C A:ASP129 5.0 37.2 1.0

Sodium binding site 3 out of 3 in the Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pantothenate Kinase From Mycobacterium Tuberculosis (Mtpank) in Complex with Adp and Pantothenate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na710 b:46.6 occ:1.00 O3 A:GOL701 2.5 76.6 1.0 O A:SER215 2.8 45.8 1.0 O A:HOH478 2.9 50.1 1.0 C3 A:GOL701 3.3 76.6 1.0 O A:HOH360 3.3 43.0 1.0 CD2 A:LEU206 3.7 24.7 1.0 C2 A:GOL701 3.8 76.6 1.0 C A:SER215 3.9 45.8 1.0 CB A:PHE218 3.9 31.7 1.0 CD1 A:PHE218 4.0 31.7 1.0 CB A:SER215 4.1 43.0 1.0 CA A:SER215 4.3 45.8 1.0 O A:HOH477 4.3 61.4 1.0 CG A:PHE218 4.4 31.7 1.0 O2 A:GOL701 4.5 76.6 1.0 OG A:SER221 4.5 41.3 1.0 CB A:SER221 4.7 41.3 1.0 O A:ARG291 4.8 37.0 1.0 OG A:SER215 4.9 43.0 1.0 O A:PHE218 4.9 41.1 1.0 CA A:PHE218 5.0 41.1 1.0

B.Chetnani, S.Das, P.Kumar, A.Surolia, M.Vijayan. Mycobacterium Tuberculosis Pantothenate Kinase: Possible Changes in Location of Ligands During Enzyme Action Acta Crystallogr.,Sect.D V. 65 312 2009.
ISSN: ISSN 0907-4449
PubMed: 19307712
DOI: 10.1107/S0907444909002170