Magnesium in PDB 6o0g: M.Tb Mend Bound to Intermediate I and Inhibitor

All present enzymatic activity of M.Tb Mend Bound to Intermediate I and Inhibitor:
2.2.1.9;

The structure of M.Tb Mend Bound to Intermediate I and Inhibitor, PDB code: 6o0g was solved by J.M.Johnston, G.Bashiri, E.M.M.Bulloch, E.M.N.Jirgis, H.Chuang, L.V.Nigon, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.33 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	100.674, 143.452, 172.741, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.1

The structure of M.Tb Mend Bound to Intermediate I and Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the M.Tb Mend Bound to Intermediate I and Inhibitor (pdb code 6o0g). 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 Bound to Intermediate I and Inhibitor, PDB code: 6o0g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the M.Tb Mend Bound to Intermediate I and 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 Bound to Intermediate I and Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:33.6 occ:1.00 O21 D:TOG601 1.9 38.3 1.0 O13 D:TOG601 2.0 41.4 1.0 O D:HOH709 2.1 32.5 1.0 O D:GLY471 2.2 51.6 1.0 OD1 D:ASP440 2.2 38.0 1.0 OD1 D:ASP469 2.3 48.4 1.0 P2 D:TOG601 2.9 44.5 1.0 P1 D:TOG601 3.1 36.4 1.0 O11 D:TOG601 3.2 41.6 1.0 CG D:ASP440 3.3 41.4 1.0 O22 D:TOG601 3.3 41.9 1.0 CG D:ASP469 3.3 47.2 1.0 C D:GLY471 3.4 45.8 1.0 OD2 D:ASP469 3.7 47.4 1.0 OD2 D:ASP440 3.7 41.0 1.0 N D:GLY473 3.8 38.9 1.0 O5G D:TOG601 3.9 40.1 1.0 N D:ASP440 4.0 39.8 1.0 CA D:GLY472 4.0 36.8 1.0 N D:GLY472 4.2 40.3 1.0 O23 D:TOG601 4.2 38.3 1.0 N D:ASP469 4.3 44.5 1.0 O D:SER467 4.3 47.2 1.0 N D:GLY471 4.3 48.3 1.0 O12 D:TOG601 4.4 40.4 1.0 C D:GLY472 4.5 37.7 1.0 CA D:GLY471 4.5 47.3 1.0 CB D:ASP440 4.5 41.7 1.0 CA D:GLY439 4.5 38.6 1.0 O D:HOH731 4.5 34.4 1.0 N D:LEU441 4.6 40.4 1.0 CB D:ASP469 4.6 45.8 1.0 C D:GLY439 4.7 39.8 1.0 CA D:ASP440 4.8 39.4 1.0 C D:ASP469 4.8 45.1 1.0 CA D:ASP469 4.8 45.9 1.0 CA D:GLY473 4.8 40.3 1.0 N D:ASN470 4.9 44.0 1.0

Magnesium binding site 2 out of 2 in the M.Tb Mend Bound to Intermediate I and 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 Bound to Intermediate I and Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:34.0 occ:1.00 O21 C:TOG601 1.9 38.2 1.0 O C:HOH705 2.0 29.1 1.0 OD1 C:ASP469 2.0 57.2 1.0 OD1 C:ASP440 2.1 50.1 1.0 O C:GLY471 2.1 57.9 1.0 O13 C:TOG601 2.2 50.4 1.0 CG C:ASP440 3.0 48.8 1.0 P2 C:TOG601 3.2 45.0 1.0 CG C:ASP469 3.2 57.3 1.0 OD2 C:ASP440 3.3 48.0 1.0 C C:GLY471 3.4 55.1 1.0 P1 C:TOG601 3.4 50.0 1.0 O11 C:TOG601 3.6 49.6 1.0 OD2 C:ASP469 3.7 57.5 1.0 O22 C:TOG601 3.7 43.1 1.0 N C:ASP440 3.8 47.7 1.0 N C:GLY473 4.0 60.3 1.0 N C:GLY471 4.0 48.6 1.0 N C:ASP469 4.1 54.1 1.0 O5G C:TOG601 4.2 44.7 1.0 CB C:ASP440 4.3 45.9 1.0 N C:GLY472 4.3 54.4 1.0 O C:SER467 4.3 48.5 1.0 CA C:GLY472 4.3 54.5 1.0 CA C:GLY471 4.3 50.4 1.0 O C:HOH728 4.3 49.8 1.0 O23 C:TOG601 4.4 43.2 1.0 CB C:ASP469 4.4 56.3 1.0 CA C:GLY439 4.4 43.0 1.0 N C:LEU441 4.4 43.1 1.0 C C:ASP469 4.5 50.9 1.0 CA C:ASP440 4.5 46.1 1.0 C C:GLY439 4.6 46.6 1.0 O12 C:TOG601 4.6 52.0 1.0 CA C:ASP469 4.6 53.5 1.0 N C:ASN470 4.6 49.7 1.0 C C:GLY472 4.7 58.1 1.0 O C:ASP469 4.9 50.2 1.0 CA C:GLY473 5.0 56.9 1.0 CD1 C:LEU441 5.0 44.8 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