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Magnesium in PDB 5ess: Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct)

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

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

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct), PDB code: 5ess 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) 19.73 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.144, 143.551, 174.289, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct) (pdb code 5ess). 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 I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct), PDB code: 5ess:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5ess

Go back to Magnesium Binding Sites List in 5ess
Magnesium binding site 1 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate 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 I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:70.0
occ:1.00
 O5 A:DPO606 1.7 86.8 0.7
OD1 A:ASP440 2.0 58.6 1.0
OD1 A:ASP469 2.0 78.5 1.0
O3 A:DPO606 2.4 71.4 0.7
O A:GLY471 2.7 86.0 1.0
P2 A:DPO606 3.1 89.1 0.7
CG A:ASP440 3.1 58.5 1.0
CG A:ASP469 3.1 78.6 1.0
P1 A:DPO606 3.6 67.4 0.7
OD2 A:ASP469 3.6 76.8 1.0
OD2 A:ASP440 3.7 58.8 1.0
O4 A:DPO606 3.7 84.2 0.7
O7 A:DPO606 3.7 75.0 0.7
N A:ASP440 3.7 49.5 1.0
C A:GLY471 3.7 80.3 1.0
CA A:GLY472 4.0 88.2 1.0
N A:ASP469 4.0 58.5 1.0
O A:SER467 4.0 54.1 1.0
CB A:ASP440 4.2 48.3 1.0
N A:LEU441 4.2 49.7 1.0
O6 A:DPO606 4.3 86.7 0.7
N A:GLY472 4.3 79.3 1.0
N A:GLY473 4.4 0.2 1.0
C A:GLY472 4.4 97.1 1.0
CB A:ASP469 4.4 66.4 1.0
CA A:ASP440 4.4 50.4 1.0
N A:GLY471 4.5 67.6 1.0
C A:GLY439 4.5 50.4 1.0
CA A:GLY439 4.5 45.5 1.0
CA A:ASP469 4.6 60.0 1.0
O1 A:DPO606 4.6 74.2 0.7
O2 A:DPO606 4.6 55.6 0.7
C A:ASP469 4.6 65.6 1.0
N A:ASN470 4.7 63.8 1.0
CA A:GLY471 4.7 74.4 1.0
C A:ASP440 4.8 50.8 1.0
CG A:LEU441 4.9 67.3 1.0

Magnesium binding site 2 out of 3 in 5ess

Go back to Magnesium Binding Sites List in 5ess
Magnesium binding site 2 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate 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 I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:43.6
occ:1.00
 O13 C:TOG601 2.0 52.2 1.0
O21 C:TOG601 2.0 48.1 1.0
OD1 C:ASP440 2.0 49.6 1.0
O C:GLY471 2.1 43.7 1.0
O C:HOH730 2.1 43.6 1.0
OD1 C:ASP469 2.2 49.4 1.0
CG C:ASP440 3.0 47.1 1.0
P2 C:TOG601 3.1 49.0 1.0
P1 C:TOG601 3.2 42.1 1.0
CG C:ASP469 3.3 52.6 1.0
C C:GLY471 3.3 49.1 1.0
O11 C:TOG601 3.4 47.0 1.0
OD2 C:ASP440 3.5 44.5 1.0
OD2 C:ASP469 3.7 45.2 1.0
O22 C:TOG601 3.7 44.0 1.0
N C:ASP440 3.8 47.0 1.0
N C:GLY473 3.9 50.2 1.0
O5G C:TOG601 4.0 43.8 1.0
N C:GLY471 4.1 48.8 1.0
N C:GLY472 4.2 45.9 1.0
CA C:GLY472 4.2 48.5 1.0
N C:ASP469 4.2 48.7 1.0
CB C:ASP440 4.3 39.8 1.0
CA C:GLY471 4.3 45.7 1.0
O12 C:TOG601 4.3 50.9 1.0
O C:SER467 4.4 56.0 1.0
N C:LEU441 4.4 45.3 1.0
O23 C:TOG601 4.4 46.6 1.0
CA C:GLY439 4.5 39.7 1.0
CA C:ASP440 4.5 49.1 1.0
C C:GLY472 4.5 51.6 1.0
CB C:ASP469 4.6 52.3 1.0
C C:GLY439 4.6 47.8 1.0
C C:ASP469 4.7 48.5 1.0
CA C:ASP469 4.7 49.5 1.0
N C:ASN470 4.8 52.1 1.0
CG C:LEU441 4.8 53.8 1.0
CA C:GLY473 4.8 50.2 1.0
C C:ASP440 5.0 41.8 1.0

Magnesium binding site 3 out of 3 in 5ess

Go back to Magnesium Binding Sites List in 5ess
Magnesium binding site 3 out of 3 in the Crystal Structure of M. Tuberculosis Mend Bound to MG2+ and Covalent Intermediate I (A Thdp and Decarboxylated 2-Oxoglutarate 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 I (A Thdp and Decarboxylated 2-Oxoglutarate Adduct) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:37.7
occ:1.00
 O D:HOH719 2.0 36.6 1.0
O21 D:TOG601 2.0 41.6 1.0
O13 D:TOG601 2.0 41.9 1.0
O D:GLY471 2.1 38.8 1.0
OD1 D:ASP469 2.1 51.8 1.0
OD1 D:ASP440 2.1 45.2 1.0
CG D:ASP440 3.1 42.9 1.0
CG D:ASP469 3.2 51.9 1.0
P2 D:TOG601 3.2 43.2 1.0
P1 D:TOG601 3.2 39.0 1.0
C D:GLY471 3.3 41.5 1.0
O11 D:TOG601 3.4 41.9 1.0
OD2 D:ASP440 3.5 45.8 1.0
OD2 D:ASP469 3.6 45.3 1.0
N D:GLY473 3.8 43.3 1.0
O22 D:TOG601 3.8 42.3 1.0
N D:ASP440 3.9 39.3 1.0
O5G D:TOG601 4.0 43.3 1.0
N D:GLY471 4.1 44.1 1.0
N D:GLY472 4.2 38.5 1.0
CA D:GLY472 4.2 36.3 1.0
N D:ASP469 4.2 42.5 1.0
CA D:GLY471 4.3 36.5 1.0
CB D:ASP440 4.4 38.8 1.0
O23 D:TOG601 4.4 40.2 1.0
O12 D:TOG601 4.4 39.0 1.0
O D:SER467 4.4 46.5 1.0
CB D:ASP469 4.5 42.5 1.0
N D:LEU441 4.5 39.1 1.0
C D:GLY472 4.5 37.7 1.0
C D:ASP469 4.6 40.6 1.0
CA D:ASP469 4.7 42.7 1.0
CA D:ASP440 4.7 41.7 1.0
CA D:GLY439 4.7 36.6 1.0
CA D:GLY473 4.7 42.0 1.0
N D:ASN470 4.8 43.6 1.0
C D:GLY439 4.8 39.7 1.0
CG D:LEU441 4.8 50.0 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 03:54:51 2024

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