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Magnesium in PDB 5esu: Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct)

Enzymatic activity of Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct)

All present enzymatic activity of Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct):
2.2.1.9;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct), PDB code: 5esu 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) 19.85 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.450, 139.825, 183.322, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct) (pdb code 5esu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct), PDB code: 5esu:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5esu

Go back to Magnesium Binding Sites List in 5esu
Magnesium binding site 1 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct)


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 Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:56.4
occ:1.00
 OD1 A:ASP469 2.1 68.3 1.0
O1 A:FMT602 2.5 63.4 1.0
OD1 A:ASP440 2.6 52.0 1.0
O A:HOH727 2.6 60.5 1.0
N A:GLY472 3.1 80.9 1.0
C A:GLY472 3.1 74.0 1.0
CG A:ASP469 3.1 69.0 1.0
OD2 A:ASP469 3.4 69.3 1.0
CG A:ASP440 3.5 54.8 1.0
CA A:GLY472 3.6 77.0 1.0
C A:FMT602 3.7 53.5 1.0
OD2 A:ASP440 3.9 58.6 1.0
N A:GLY471 4.0 69.5 1.0
N A:ASP440 4.1 42.2 1.0
O A:GLY472 4.1 71.1 1.0
C A:GLY471 4.1 80.9 1.0
CA A:GLY471 4.3 72.5 1.0
O A:SER467 4.4 47.9 1.0
O2 A:FMT602 4.4 55.5 1.0
N A:ASP469 4.4 58.4 1.0
CB A:ASP469 4.5 67.4 1.0
N A:LEU441 4.5 41.2 1.0
CA A:GLY439 4.7 38.9 1.0
CB A:ASP440 4.7 41.8 1.0
N A:ASN470 4.7 69.4 1.0
CG A:LEU441 4.7 69.2 1.0
CD1 A:LEU441 4.8 66.9 1.0
CA A:ASP469 4.8 59.2 1.0
C A:GLY439 4.8 46.5 1.0
C A:ASP469 4.8 60.6 1.0
CA A:ASP440 4.9 40.3 1.0
ND2 A:ASN378 4.9 59.7 1.0
CB A:LEU441 5.0 42.9 1.0

Magnesium binding site 2 out of 3 in 5esu

Go back to Magnesium Binding Sites List in 5esu
Magnesium binding site 2 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct)


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 Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:42.2
occ:1.00
 OD1 C:ASP440 2.0 48.2 1.0
O21 C:TOI601 2.0 44.2 1.0
OD1 C:ASP469 2.1 51.8 1.0
O C:HOH724 2.1 44.0 1.0
O13 C:TOI601 2.2 53.9 1.0
O C:GLY471 2.2 47.9 1.0
CG C:ASP440 3.1 53.5 1.0
CG C:ASP469 3.1 52.9 1.0
P2 C:TOI601 3.2 55.4 1.0
P1 C:TOI601 3.4 47.9 1.0
C C:GLY471 3.4 54.5 1.0
OD2 C:ASP469 3.5 47.4 1.0
O11 C:TOI601 3.5 53.7 1.0
OD2 C:ASP440 3.7 49.9 1.0
O22 C:TOI601 3.8 50.3 1.0
N C:ASP440 3.8 44.0 1.0
N C:GLY471 4.1 50.9 1.0
N C:GLY473 4.1 57.3 1.0
N C:ASP469 4.1 50.6 1.0
O C:SER467 4.2 52.5 1.0
O5G C:TOI601 4.2 54.6 1.0
CB C:ASP440 4.3 38.4 1.0
CA C:GLY471 4.3 44.2 1.0
N C:GLY472 4.3 57.4 1.0
CA C:GLY472 4.4 51.4 1.0
CB C:ASP469 4.4 53.3 1.0
O23 C:TOI601 4.5 48.5 1.0
N C:LEU441 4.5 52.9 1.0
CA C:GLY439 4.6 43.2 1.0
O12 C:TOI601 4.6 58.1 1.0
CA C:ASP440 4.6 45.6 1.0
CA C:ASP469 4.6 48.2 1.0
O C:HOH735 4.7 47.6 1.0
C C:GLY439 4.7 46.4 1.0
C C:ASP469 4.7 47.9 1.0
N C:ASN470 4.7 49.6 1.0
C C:GLY472 4.8 59.3 1.0
CD1 C:LEU441 4.9 49.4 1.0

Magnesium binding site 3 out of 3 in 5esu

Go back to Magnesium Binding Sites List in 5esu
Magnesium binding site 3 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct)


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 Bound to MG2+ and Covalent Intermediate II (A Thdp + De-Carboxylated 2-Oxoglutarate + Isochorismate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:33.9
occ:1.00
 O21 D:TOI602 2.0 35.2 1.0
O13 D:TOI602 2.0 36.1 1.0
O D:HOH755 2.0 28.4 1.0
OD1 D:ASP440 2.1 34.4 1.0
O D:GLY471 2.1 30.8 1.0
OD1 D:ASP469 2.2 35.8 1.0
CG D:ASP440 3.1 30.5 1.0
P2 D:TOI602 3.1 35.3 1.0
P1 D:TOI602 3.2 34.5 1.0
CG D:ASP469 3.2 41.8 1.0
C D:GLY471 3.4 37.3 1.0
O11 D:TOI602 3.4 33.8 1.0
OD2 D:ASP469 3.6 39.2 1.0
OD2 D:ASP440 3.6 29.1 1.0
O22 D:TOI602 3.7 32.4 1.0
N D:ASP440 3.8 36.9 1.0
N D:GLY473 4.0 35.1 1.0
O5G D:TOI602 4.1 36.8 1.0
N D:GLY471 4.1 33.6 1.0
N D:ASP469 4.2 36.9 1.0
N D:GLY472 4.2 36.7 1.0
CA D:GLY472 4.3 35.8 1.0
O D:SER467 4.3 36.3 1.0
CB D:ASP440 4.3 34.8 1.0
CA D:GLY471 4.3 35.8 1.0
N D:LEU441 4.4 27.5 1.0
O12 D:TOI602 4.4 34.9 1.0
O23 D:TOI602 4.4 33.9 1.0
CA D:GLY439 4.5 32.6 1.0
CB D:ASP469 4.5 42.6 1.0
CA D:ASP440 4.6 33.8 1.0
C D:GLY439 4.6 34.8 1.0
C D:GLY472 4.7 40.8 1.0
O D:HOH751 4.7 37.5 1.0
CA D:ASP469 4.7 33.7 1.0
C D:ASP469 4.7 40.7 1.0
N D:ASN470 4.8 35.2 1.0
O D:HOH701 4.8 41.4 1.0
CD1 D:LEU441 5.0 34.5 1.0
CA D:GLY473 5.0 35.8 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: Sun Sep 29 03:55:31 2024

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