Magnesium in PDB 7ugw: M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin

All present enzymatic activity of M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin:
5.6.2.2;

The structure of M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin, PDB code: 7ugw was solved by G.Hauk, Y.Imai, K.Lewis, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.46 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.075, 105.088, 250.183, 90, 90, 90
R / Rfree (%)	20.1 / 28.6

The binding sites of Magnesium atom in the M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin (pdb code 7ugw). 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. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin, PDB code: 7ugw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:31.9 occ:1.00 OD2 B:ASP534 2.2 48.3 1.0 OD2 B:ASP532 2.6 33.7 1.0 H5'' V:DG46 3.4 37.0 1.0 CG B:ASP534 3.5 42.3 1.0 CG B:ASP532 3.8 40.4 1.0 O B:LYS611 3.9 35.4 1.0 OP1 V:DG46 3.9 28.3 1.0 H5' V:DG46 4.1 37.0 1.0 HB3 B:ASP532 4.1 56.8 1.0 HA3 B:GLY612 4.2 58.1 1.0 OD1 B:ASP534 4.2 48.3 1.0 C5' V:DG46 4.2 30.9 1.0 HB2 B:ASP532 4.3 56.8 1.0 CB B:ASP532 4.4 47.3 1.0 HB3 B:ASP534 4.4 42.4 1.0 CB B:ASP534 4.5 35.4 1.0 HB2 B:ASP536 4.6 37.6 1.0 H3' V:DG46 4.7 40.5 1.0 HB2 B:ASP534 4.7 42.4 1.0 OD1 B:ASP532 4.7 36.0 1.0 HE1 C:PHE129 4.8 45.5 1.0 HD1 A:HIS87 4.8 44.3 1.0 CA B:GLY612 5.0 48.5 1.0 HA2 B:GLY612 5.0 58.1 1.0 O A:PRO86 5.0 28.4 1.0 OE2 B:GLU459 5.0 38.1 1.0 C B:LYS611 5.0 43.5 1.0

Magnesium binding site 2 out of 2 in the M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of M. Tuberculosis Dna Gyrase Cleavage Core Bound to Dna and Evybactin within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg101 b:41.3 occ:1.00 N7 V:DG32 3.8 59.4 1.0 OE1 B:GLU654 4.1 76.2 1.0 O6 V:DG33 4.3 51.3 1.0 N7 V:DG33 4.3 60.5 1.0 C8 V:DG32 4.5 54.0 1.0 H8 V:DG32 4.5 64.9 1.0 C5 V:DG32 4.6 53.2 1.0 O6 V:DG40 4.6 63.1 1.0 O6 V:DG32 4.7 67.9 1.0 OE2 B:GLU654 4.7 79.0 1.0 CD B:GLU654 4.9 67.5 1.0 HD3 B:LYS490 4.9 58.3 1.0 C6 V:DG32 4.9 55.1 1.0 H41 V:DC34 5.0 91.5 1.0 H42 V:DC34 5.0 91.5 1.0

Y.Imai, G.Hauk, J.Quigley, L.Liang, S.Son, M.Ghiglieri, M.F.Gates, M.Morrissette, N.Shahsavari, S.Niles, D.Baldisseri, C.Honrao, X.Ma, J.J.Guo, J.M.Berger, K.Lewis. Evybactin Is A Dna Gyrase Inhibitor That Selectively Kills Mycobacterium Tuberculosis. Nat.Chem.Biol. V. 18 1236 2022.
ISSN: ESSN 1552-4469
PubMed: 35996001
DOI: 10.1038/S41589-022-01102-7