Magnesium in PDB 6o0j: M.Tb Mend with Thdp and Inhibitor Bound

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

The structure of M.Tb Mend with Thdp and Inhibitor Bound, PDB code: 6o0j was solved by J.M.Johnston, G.Bashiri, E.M.M.Bulloch, E.M.N.Jirgis, L.V.Nigon, H.Chuang, N.A.T.Ho, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.553, 143.673, 176.114, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.1

The binding sites of Magnesium atom in the M.Tb Mend with Thdp and Inhibitor Bound (pdb code 6o0j). 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 with Thdp and Inhibitor Bound, PDB code: 6o0j:
Jump to Magnesium binding site number: 1; 2;

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


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 with Thdp and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:37.6 occ:1.00 O22 D:TDP604 1.8 41.2 1.0 OD1 D:ASP469 2.0 65.1 1.0 O D:HOH717 2.1 46.0 1.0 O13 D:TDP604 2.2 47.1 1.0 O D:GLY471 2.2 49.7 1.0 OD1 D:ASP440 2.3 54.4 1.0 CG D:ASP469 3.0 59.5 1.0 P2 D:TDP604 3.1 46.7 1.0 CG D:ASP440 3.3 49.8 1.0 P1 D:TDP604 3.4 43.0 1.0 OD2 D:ASP469 3.4 59.0 1.0 C D:GLY471 3.4 45.2 1.0 O11 D:TDP604 3.5 44.4 1.0 OD2 D:ASP440 3.6 49.0 1.0 O21 D:TDP604 3.7 43.4 1.0 N D:GLY473 3.8 43.8 1.0 N D:ASP440 4.1 47.4 1.0 N D:ASP469 4.1 51.9 1.0 CA D:GLY472 4.2 40.6 1.0 O5G D:TDP604 4.2 43.1 1.0 O23 D:TDP604 4.3 47.4 1.0 N D:GLY471 4.3 50.6 1.0 N D:GLY472 4.3 40.8 1.0 O D:SER467 4.3 41.9 1.0 CB D:ASP469 4.3 55.4 1.0 CA D:GLY471 4.5 46.5 1.0 O D:HOH763 4.5 49.3 1.0 C D:GLY472 4.5 43.0 1.0 O12 D:TDP604 4.5 47.7 1.0 CB D:ASP440 4.6 48.7 1.0 CA D:ASP469 4.6 53.6 1.0 C D:ASP469 4.6 52.6 1.0 CA D:GLY439 4.7 41.4 1.0 CA D:GLY473 4.8 43.4 1.0 N D:ASN470 4.8 49.3 1.0 N D:LEU441 4.8 41.6 1.0 CA D:ASP440 4.9 47.9 1.0 C D:GLY439 4.9 45.6 1.0

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


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 with Thdp and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:41.4 occ:1.00 OD1 C:ASP469 2.0 72.6 1.0 O21 C:TDP604 2.0 43.5 1.0 O C:HOH704 2.1 36.4 1.0 O12 C:TDP604 2.1 47.6 1.0 OD1 C:ASP440 2.3 52.5 1.0 O C:GLY471 2.3 47.7 1.0 P2 C:TDP604 2.9 48.0 1.0 CG C:ASP469 3.0 70.3 1.0 O23 C:TDP604 3.1 43.1 1.0 CG C:ASP440 3.2 53.2 1.0 OD2 C:ASP469 3.3 70.5 1.0 P1 C:TDP604 3.3 49.0 1.0 O11 C:TDP604 3.4 50.3 1.0 C C:GLY471 3.5 52.1 1.0 OD2 C:ASP440 3.6 52.9 1.0 N C:GLY473 3.8 57.8 1.0 N C:ASP440 4.0 42.5 1.0 N C:ASP469 4.2 56.5 1.0 O5G C:TDP604 4.2 47.4 1.0 CA C:GLY472 4.2 51.6 1.0 O C:SER467 4.3 49.5 1.0 O22 C:TDP604 4.3 49.4 1.0 CB C:ASP469 4.3 66.7 1.0 N C:GLY472 4.3 54.2 1.0 N C:GLY471 4.4 52.3 1.0 O13 C:TDP604 4.5 49.2 1.0 C C:GLY472 4.5 56.2 1.0 CB C:ASP440 4.5 51.4 1.0 CA C:GLY471 4.6 51.9 1.0 CA C:GLY439 4.6 44.6 1.0 CA C:ASP469 4.6 60.4 1.0 CA C:GLY473 4.7 57.0 1.0 C C:ASP469 4.7 56.2 1.0 C C:GLY439 4.8 44.0 1.0 N C:ASN470 4.8 52.0 1.0 CA C:ASP440 4.8 45.0 1.0 N C:LEU441 4.9 43.8 1.0 O C:HOH757 4.9 47.9 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