Magnesium in PDB 5eso: Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound

Enzymatic activity of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound

All present enzymatic activity of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound:
2.2.1.9;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound, PDB code: 5eso was solved by J.M.Johnston, E.N.M.Jirgis, G.Bashiri, E.M.M.Bulloch, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.444, 139.592, 181.768, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound (pdb code 5eso). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound, PDB code: 5eso:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5eso

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Magnesium binding site 1 out of 4 in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:50.2
occ:1.00
 O A:HOH899 2.2 66.9 1.0
O A:HOH835 2.2 57.5 1.0
O A:HOH823 2.3 60.6 1.0
O A:HOH904 2.4 66.5 1.0
OD1 A:ASP469 2.5 61.3 1.0
OD1 A:ASP440 2.9 55.7 1.0
CG A:ASP469 3.6 64.0 1.0
OD2 A:ASP469 3.9 70.1 1.0
CG A:ASP440 4.0 60.5 1.0
O A:ASN470 4.1 71.7 1.0
O A:HOH801 4.3 51.1 1.0
O A:HOH905 4.3 55.1 1.0
OD2 A:ASP440 4.4 63.6 1.0
N A:ASP440 4.4 45.3 1.0
O A:HOH921 4.4 66.3 1.0
N A:LEU441 4.5 43.8 1.0
O A:HOH920 4.7 56.9 1.0
N A:ASP469 4.7 50.6 1.0
CB A:LEU441 4.7 51.4 1.0
O A:HOH923 4.8 56.2 1.0
O A:SER467 4.8 46.5 1.0
N A:ASN470 4.9 66.8 1.0
CB A:ASP469 4.9 58.1 1.0
CA A:GLY439 4.9 47.5 1.0
C A:ASP469 5.0 66.0 1.0
C A:ASN470 5.0 76.2 1.0

Magnesium binding site 2 out of 4 in 5eso

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Magnesium binding site 2 out of 4 in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:52.0
occ:1.00
 O B:HOH850 2.1 63.1 1.0
OD1 B:ASP469 2.2 70.3 1.0
O B:GLY471 2.3 75.3 1.0
O1 B:FMT604 2.6 55.6 1.0
OD1 B:ASP440 2.7 53.6 1.0
O B:HOH701 2.8 64.9 1.0
CG B:ASP469 3.1 66.8 1.0
OD2 B:ASP469 3.3 70.1 1.0
C B:GLY471 3.5 73.2 1.0
C B:FMT604 3.6 51.5 1.0
CG B:ASP440 3.8 50.5 1.0
O2 B:FMT604 3.8 61.9 1.0
N B:ASP440 4.2 41.6 1.0
N B:GLY471 4.3 68.2 1.0
OD2 B:ASP440 4.3 56.6 1.0
CA B:GLY471 4.3 69.2 1.0
N B:ASP469 4.5 55.4 1.0
CB B:ASP469 4.5 61.5 1.0
O B:SER467 4.5 46.3 1.0
N B:LEU441 4.6 46.5 1.0
CA B:GLY439 4.7 39.3 1.0
CA B:ASP469 4.9 57.1 1.0
C B:GLY439 4.9 46.1 1.0
C B:ASP469 4.9 65.5 1.0
CB B:ASP440 5.0 48.8 1.0

Magnesium binding site 3 out of 4 in 5eso

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Magnesium binding site 3 out of 4 in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:32.1
occ:1.00
 O C:HOH730 2.0 29.8 1.0
O12 C:TDP605 2.0 35.7 1.0
O C:GLY471 2.0 34.9 1.0
OD1 C:ASP440 2.1 34.9 1.0
O21 C:TDP605 2.1 34.5 1.0
OD1 C:ASP469 2.1 37.0 1.0
CG C:ASP440 3.1 32.8 1.0
CG C:ASP469 3.2 42.5 1.0
P2 C:TDP605 3.2 35.1 1.0
P1 C:TDP605 3.3 33.1 1.0
C C:GLY471 3.3 37.7 1.0
O11 C:TDP605 3.5 31.9 1.0
OD2 C:ASP440 3.5 32.9 1.0
OD2 C:ASP469 3.6 44.0 1.0
O22 C:TDP605 3.7 35.1 1.0
N C:ASP440 3.8 35.0 1.0
N C:GLY473 4.0 33.5 1.0
N C:GLY471 4.0 35.8 1.0
O5G C:TDP605 4.1 35.6 1.0
N C:GLY472 4.1 41.1 1.0
N C:ASP469 4.2 38.6 1.0
CA C:GLY472 4.2 36.5 1.0
CA C:GLY471 4.3 36.1 1.0
CB C:ASP440 4.3 33.6 1.0
O C:SER467 4.4 42.0 1.0
N C:LEU441 4.4 30.0 1.0
CB C:ASP469 4.4 45.9 1.0
O13 C:TDP605 4.5 35.5 1.0
O23 C:TDP605 4.5 33.4 1.0
CA C:GLY439 4.5 33.6 1.0
CA C:ASP440 4.6 35.9 1.0
C C:GLY472 4.6 35.5 1.0
C C:GLY439 4.6 35.6 1.0
CA C:ASP469 4.6 36.4 1.0
C C:ASP469 4.6 36.8 1.0
O C:HOH731 4.7 36.6 1.0
N C:ASN470 4.7 38.5 1.0
CA C:GLY473 5.0 37.3 1.0

Magnesium binding site 4 out of 4 in 5eso

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Magnesium binding site 4 out of 4 in the Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of M. Tuberculosis Mend with Thdp, MG2+ and Isochorismate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:42.3
occ:1.00
 OD1 D:ASP440 1.9 46.4 1.0
O D:GLY471 2.0 45.8 1.0
O13 D:TDP602 2.0 52.5 1.0
O D:HOH715 2.1 46.3 1.0
O22 D:TDP602 2.1 47.3 1.0
OD1 D:ASP469 2.2 52.6 1.0
CG D:ASP440 3.0 44.0 1.0
CG D:ASP469 3.1 48.7 1.0
C D:GLY471 3.2 47.6 1.0
P2 D:TDP602 3.2 56.8 1.0
P1 D:TDP602 3.3 45.7 1.0
OD2 D:ASP440 3.5 43.8 1.0
OD2 D:ASP469 3.5 50.5 1.0
O11 D:TDP602 3.5 54.1 1.0
O21 D:TDP602 3.7 50.0 1.0
N D:ASP440 3.8 48.7 1.0
N D:GLY473 4.0 50.4 1.0
N D:GLY471 4.0 50.8 1.0
O5G D:TDP602 4.1 49.4 1.0
N D:GLY472 4.1 49.2 1.0
CA D:GLY472 4.1 50.6 1.0
N D:ASP469 4.1 45.1 1.0
CB D:ASP440 4.2 43.8 1.0
CA D:GLY471 4.2 46.2 1.0
O D:SER467 4.3 51.0 1.0
CB D:ASP469 4.4 49.1 1.0
N D:LEU441 4.5 48.3 1.0
O12 D:TDP602 4.5 50.3 1.0
CA D:ASP440 4.5 47.1 1.0
O23 D:TDP602 4.5 42.9 1.0
C D:GLY472 4.6 49.9 1.0
CA D:GLY439 4.6 44.7 1.0
CA D:ASP469 4.6 43.6 1.0
C D:ASP469 4.7 45.4 1.0
C D:GLY439 4.7 46.1 1.0
N D:ASN470 4.8 44.2 1.0
CA D:GLY473 5.0 51.3 1.0

Reference:

E.N.Jirgis, G.Bashiri, E.M.Bulloch, J.M.Johnston, E.N.Baker. Structural Views Along the Mycobacterium Tuberculosis Mend Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure V. 24 1167 2016.
ISSN: ISSN 0969-2126
PubMed: 27291649
DOI: 10.1016/J.STR.2016.04.018
Page generated: Mon Dec 14 20:16:00 2020

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