Magnesium in PDB 2iyx: Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4

All present enzymatic activity of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4:
2.7.1.71;

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4, PDB code: 2iyx was solved by M.D.Hartmann, G.P.Bourenkov, A.Oberschall, N.Strizhov, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.51 / 1.49
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.245, 59.245, 102.797, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.6

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4 (pdb code 2iyx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4, PDB code: 2iyx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:53.0 occ:1.00 OE2 A:GLU38 2.1 25.4 1.0 O A:HOH2105 2.3 16.5 1.0 CD A:GLU38 3.2 28.4 1.0 O A:HOH2079 3.4 51.2 1.0 N A:ILE45 3.6 12.8 1.0 OE1 A:GLU38 3.6 30.0 1.0 CB A:SER44 3.8 22.7 0.7 OG A:SER44 3.8 19.2 0.3 CB A:SER44 3.9 7.5 0.3 CA A:SER44 4.0 15.1 1.0 O A:HOH2104 4.1 20.3 1.0 O A:HOH2030 4.2 48.3 1.0 O A:HOH2190 4.3 21.2 1.0 C A:SER44 4.3 13.5 1.0 CB A:ILE45 4.3 14.7 1.0 CG A:GLU38 4.5 17.3 1.0 CA A:ILE45 4.5 12.9 1.0 N A:ALA46 4.6 12.2 1.0 CG1 A:ILE45 4.8 23.7 1.0 OG A:SER44 4.9 12.5 0.7

Magnesium binding site 2 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:26.5 occ:0.70 OE2 A:GLU56 2.2 22.2 0.7 O A:HOH2130 2.8 24.9 0.7 CD A:GLU56 3.0 19.6 0.7 OE1 A:GLU56 3.1 24.1 0.7 CG A:GLU56 3.8 20.7 0.3 OE2 A:GLU56 3.8 25.6 0.3 CD A:GLU56 3.9 18.1 0.3 O A:HOH2135 4.0 35.7 1.0 CG1 A:ILE60 4.2 17.8 1.0 CG A:GLU56 4.4 23.5 0.7 OE1 A:GLU56 4.5 15.4 0.3 O A:HOH2131 4.5 26.8 0.5 CD1 A:ILE60 4.5 27.9 1.0

Magnesium binding site 3 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate and SO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:50.1 occ:0.25 O A:HOH2279 2.0 35.8 1.0 O3 A:SO4203 2.1 24.4 0.2 O1 A:SO4203 2.3 14.5 0.2 S A:SO4203 2.7 23.2 0.2 O A:HOH2034 3.5 35.3 1.0 NH1 A:ARG20 3.5 33.7 1.0 O2 A:SO4203 3.6 42.5 0.2 O4 A:SO4203 3.8 14.6 0.2 CG2 A:THR17 3.9 28.6 1.0 CB A:THR17 4.0 29.2 1.0 NE A:ARG21 4.4 23.2 0.5 NE A:ARG21 4.4 60.2 0.5 CA A:THR17 4.6 24.3 1.0 CD A:ARG20 4.6 20.4 0.5 CZ A:ARG20 4.6 44.8 1.0 O A:THR17 4.9 24.0 1.0 CD A:ARG20 4.9 42.2 0.5 CG A:ARG21 5.0 28.4 0.5

M.D.Hartmann, G.P.Bourenkov, A.Oberschall, N.Strizhov, H.D.Bartunik. Mechanism of Phosphoryl Transfer Catalyzed By Shikimate Kinase From Mycobacterium Tuberculosis. J.Mol.Biol. V. 364 411 2006.
ISSN: ISSN 0022-2836
PubMed: 17020768
DOI: 10.1016/J.JMB.2006.09.001