Magnesium in PDB 6o04: M.Tb Mend Intii Bound with Inhibitor

All present enzymatic activity of M.Tb Mend Intii Bound with Inhibitor:
2.2.1.9;

The structure of M.Tb Mend Intii Bound with Inhibitor, PDB code: 6o04 was solved by J.M.Johnston, G.Bashiri, E.M.Bulloch, E.M.N.Jirgis, L.V.Nigon, H.Chuang, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.798, 143.314, 173.616, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24

The structure of M.Tb Mend Intii Bound with Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the M.Tb Mend Intii Bound with Inhibitor (pdb code 6o04). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the M.Tb Mend Intii Bound with Inhibitor, PDB code: 6o04:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the M.Tb Mend Intii Bound with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of M.Tb Mend Intii Bound with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:35.9 occ:1.00 O13 D:TOI602 2.0 41.6 1.0 OD1 D:ASP440 2.0 39.3 1.0 O21 D:TOI602 2.1 39.1 1.0 O D:GLY471 2.1 41.6 1.0 O D:HOH716 2.1 36.5 1.0 OD1 D:ASP469 2.1 44.0 1.0 P2 D:TOI602 3.1 40.2 1.0 CG D:ASP440 3.1 33.8 1.0 P1 D:TOI602 3.2 35.8 1.0 CG D:ASP469 3.2 46.6 1.0 C D:GLY471 3.3 39.4 1.0 O22 D:TOI602 3.4 38.4 1.0 O11 D:TOI602 3.4 35.0 1.0 OD2 D:ASP440 3.7 38.6 1.0 OD2 D:ASP469 3.7 46.8 1.0 N D:ASP440 3.9 37.5 1.0 N D:GLY473 3.9 40.0 1.0 O5G D:TOI602 4.1 37.4 1.0 CA D:GLY472 4.1 33.7 1.0 N D:GLY471 4.1 31.4 1.0 N D:GLY472 4.2 31.9 1.0 N D:ASP469 4.2 43.0 1.0 CA D:GLY471 4.3 37.7 1.0 CB D:ASP440 4.3 36.9 1.0 O12 D:TOI602 4.4 36.6 1.0 O23 D:TOI602 4.4 43.1 1.0 O D:SER467 4.5 39.9 1.0 CB D:ASP469 4.5 39.6 1.0 C D:GLY472 4.6 33.8 1.0 N D:LEU441 4.6 39.5 1.0 CA D:GLY439 4.6 33.8 1.0 CA D:ASP440 4.6 35.3 1.0 C D:ASP469 4.6 39.1 1.0 CA D:ASP469 4.7 40.4 1.0 O D:HOH761 4.7 36.4 1.0 C D:GLY439 4.7 38.6 1.0 N D:ASN470 4.8 38.2 1.0 CA D:GLY473 4.9 38.4 1.0 CG D:LEU441 4.9 38.4 1.0 O D:ASP469 5.0 40.3 1.0

Magnesium binding site 2 out of 2 in the M.Tb Mend Intii Bound with Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of M.Tb Mend Intii Bound with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:38.1 occ:1.00 O21 C:TOI601 1.9 37.0 1.0 O C:GLY471 2.0 41.2 1.0 OD1 C:ASP469 2.0 48.2 1.0 OD1 C:ASP440 2.0 41.7 1.0 O C:HOH735 2.2 40.2 1.0 O13 C:TOI601 2.3 41.9 1.0 CG C:ASP440 3.1 38.0 1.0 CG C:ASP469 3.1 48.1 1.0 C C:GLY471 3.2 40.7 1.0 P2 C:TOI601 3.2 44.7 1.0 OD2 C:ASP440 3.5 36.8 1.0 P1 C:TOI601 3.5 35.0 1.0 OD2 C:ASP469 3.6 43.7 1.0 O11 C:TOI601 3.7 36.5 1.0 O22 C:TOI601 3.9 39.5 1.0 N C:ASP440 3.9 38.2 1.0 N C:GLY471 3.9 43.9 1.0 N C:GLY473 3.9 48.5 1.0 N C:ASP469 4.1 45.1 1.0 N C:GLY472 4.1 37.7 1.0 CA C:GLY471 4.2 39.8 1.0 CA C:GLY472 4.2 38.5 1.0 O5G C:TOI601 4.3 34.5 1.0 CB C:ASP440 4.3 33.1 1.0 CB C:ASP469 4.4 49.4 1.0 C C:ASP469 4.4 42.4 1.0 O23 C:TOI601 4.4 37.0 1.0 CA C:ASP469 4.5 43.7 1.0 O C:SER467 4.5 43.2 1.0 N C:ASN470 4.5 40.2 1.0 N C:LEU441 4.6 36.6 1.0 C C:GLY472 4.6 45.8 1.0 CA C:ASP440 4.6 37.0 1.0 CA C:GLY439 4.7 35.0 1.0 CG C:LEU441 4.7 41.7 1.0 O12 C:TOI601 4.8 40.6 1.0 C C:GLY439 4.8 37.9 1.0 O C:ASP469 4.8 44.8 1.0 CA C:GLY473 4.9 45.6 1.0

G.Bashiri, L.V.Nigon, E.N.M.Jirgis, N.A.T.Ho, T.Stanborough, S.S.Dawes, E.N.Baker, E.M.M.Bulloch, J.M.Johnston. Allosteric Regulation of Menaquinone (Vitamin K2) Biosynthesis in the Human Pathogenmycobacterium Tuberculosis. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32029475
DOI: 10.1074/JBC.RA119.012158