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Magnesium in PDB 2iyy: Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

Enzymatic activity of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

All present enzymatic activity of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4:
2.7.1.71;

Protein crystallography data

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4, PDB code: 2iyy 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) 19.16 / 1.62
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.349, 59.349, 102.867, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 23.3

Other elements in 2iyy:

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 (pdb code 2iyy). 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-3-Phosphate and SO4, PDB code: 2iyy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2iyy

Go back to Magnesium Binding Sites List in 2iyy
Magnesium binding site 1 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate 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-3-Phosphate and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:59.8
occ:1.00
OE2 A:GLU38 2.2 38.8 1.0
O A:HOH2088 2.2 21.9 1.0
O A:HOH2063 3.1 51.5 1.0
N A:ILE45 3.3 20.5 1.0
CD A:GLU38 3.3 43.8 1.0
OG A:SER44 3.6 26.6 0.3
CB A:SER44 3.7 23.8 0.7
CB A:SER44 3.7 21.8 0.3
CA A:SER44 3.8 23.9 1.0
OE1 A:GLU38 3.9 42.1 1.0
CG1 A:ILE45 3.9 24.5 0.5
CB A:ILE45 3.9 19.9 0.5
C A:SER44 4.0 17.6 1.0
O A:HOH2085 4.1 28.7 1.0
CB A:ILE45 4.2 25.3 0.5
CA A:ILE45 4.2 19.6 0.5
CA A:ILE45 4.2 22.4 0.5
O A:HOH2164 4.2 37.0 1.0
N A:ALA46 4.3 20.3 1.0
CG A:GLU38 4.5 23.0 1.0
CG1 A:ILE45 4.6 32.8 0.5
OG A:SER44 4.7 20.0 0.7
C A:ILE45 4.8 20.9 1.0

Magnesium binding site 2 out of 3 in 2iyy

Go back to Magnesium Binding Sites List in 2iyy
Magnesium binding site 2 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate 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-3-Phosphate and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:36.3
occ:0.70
OE2 A:GLU56 2.2 46.2 1.0
CD A:GLU56 3.1 31.3 1.0
OE1 A:GLU56 3.2 42.0 1.0
O A:HOH2112 3.7 51.3 1.0
CG1 A:ILE60 4.2 28.1 1.0
O A:HOH2099 4.4 24.4 0.5
CG A:GLU56 4.5 30.3 1.0
CD1 A:ILE60 4.5 35.8 1.0

Magnesium binding site 3 out of 3 in 2iyy

Go back to Magnesium Binding Sites List in 2iyy
Magnesium binding site 3 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate 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-3-Phosphate and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:40.9
occ:0.25
O A:HOH2236 2.0 51.1 1.0
O3 A:SO4205 2.2 17.8 0.2
O1 A:SO4205 2.4 28.6 0.2
S A:SO4205 2.8 29.6 0.2
NH1 A:ARG20 3.6 39.8 1.0
CG2 A:THR17 3.8 47.3 1.0
O4 A:SO4205 3.9 34.2 0.2
O2 A:SO4205 3.9 36.5 0.2
CB A:THR17 4.0 34.3 1.0
NE A:ARG21 4.5 27.6 0.5
NE A:ARG21 4.5 66.2 0.5
CD A:ARG20 4.6 26.5 0.5
CA A:THR17 4.6 35.6 1.0
CZ A:ARG20 4.7 55.0 1.0
CD A:ARG20 4.8 53.4 0.5
O A:THR17 4.9 32.2 1.0
CG A:ARG21 5.0 24.6 0.5

Reference:

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
Page generated: Wed Aug 14 00:20:26 2024

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