Magnesium in PDB 9drv: Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004

All present enzymatic activity of Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004:
6.1.1.20;

The structure of Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004, PDB code: 9drv was solved by P.Gade, C.Chang, B.Forte, J.Wower, I.H.Gilbert, B.Baragana, K.Michalska, A.Joachimiak, Center For Structural Biology Of Infectious Diseases(Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	147.091, 64.393, 188.776, 90, 111.1, 90
R / Rfree (%)	21 / 26

The binding sites of Magnesium atom in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004 (pdb code 9drv). 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 Phers-Trna Complex Bound to Inhibitor D-004, PDB code: 9drv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004


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 Phers-Trna Complex Bound to Inhibitor D-004 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.1 occ:1.00 O B:HOH1094 2.0 28.7 1.0 O A:HOH539 2.0 32.1 1.0 OE2 B:GLU476 2.1 35.5 1.0 O B:HOH1016 2.1 28.3 1.0 O B:HOH1087 2.1 29.0 1.0 OE2 A:GLU259 2.1 35.6 1.0 CD B:GLU476 3.1 33.6 1.0 CD A:GLU259 3.2 32.7 1.0 OE1 A:GLU259 3.6 39.6 1.0 OD2 B:ASP172 3.7 37.9 1.0 CG B:GLU476 3.8 27.7 1.0 OE1 B:GLU476 3.9 40.6 1.0 CB B:GLU476 4.1 29.3 1.0 OD2 B:ASP467 4.1 33.2 1.0 NH2 B:ARG173 4.2 29.8 1.0 OD1 B:ASP473 4.3 42.9 1.0 O B:HOH1296 4.3 35.5 1.0 O B:ASP473 4.4 26.1 1.0 OE2 B:GLU477 4.4 25.8 1.0 CA B:ASP473 4.4 27.5 1.0 CB B:ASP473 4.5 31.4 1.0 CG A:GLU259 4.5 33.2 1.0 CG B:ASP473 4.9 36.0 1.0 CG B:ASP172 4.9 27.9 1.0 C B:ASP473 4.9 25.7 1.0 CZ B:ARG173 4.9 26.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004


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 Phers-Trna Complex Bound to Inhibitor D-004 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg400 b:47.1 occ:1.00 O C:HOH509 2.1 35.9 1.0 O C:HOH522 2.3 30.3 1.0 O C:HOH510 2.6 35.3 1.0 OP2 C:U8 3.2 54.7 1.0 OP1 C:U8 3.5 52.1 1.0 OP2 C:A9 3.6 37.7 1.0 P C:U8 3.7 42.0 1.0 OP1 C:A9 4.1 37.4 1.0 O C:HOH508 4.4 27.9 1.0 P C:A9 4.4 40.8 1.0 OP2 C:U12 4.4 31.7 1.0 O5' C:U8 4.4 40.3 1.0 O C:HOH518 4.5 48.8 1.0 O C:HOH506 4.7 37.3 1.0 C5 C:C13 4.8 35.1 1.0 C5 C:U12 4.9 28.9 1.0 OP2 C:C11 5.0 34.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of M. Tuberculosis Phers-Trna Complex Bound to Inhibitor D-004


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 Phers-Trna Complex Bound to Inhibitor D-004 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:42.8 occ:1.00 O D:HOH511 2.0 40.9 1.0 OE2 E:GLU476 2.0 40.9 1.0 O E:HOH1012 2.1 34.2 1.0 O E:HOH1022 2.1 32.6 1.0 OE2 D:GLU259 2.9 42.1 1.0 CD E:GLU476 3.2 43.7 1.0 OD2 E:ASP172 3.3 49.4 1.0 OD2 E:ASP467 3.4 48.0 1.0 CD D:GLU259 3.9 40.1 1.0 OE2 E:GLU477 4.0 32.0 1.0 OE1 E:GLU476 4.0 43.0 1.0 CG E:GLU476 4.0 31.6 1.0 NH1 E:ARG173 4.1 41.1 1.0 OE1 D:GLU259 4.1 40.5 1.0 NH2 E:ARG173 4.3 36.3 1.0 NH2 E:ARG465 4.3 30.6 1.0 CB E:GLU476 4.4 35.4 1.0 CG E:ASP172 4.4 39.2 1.0 CZ E:ARG173 4.5 41.1 1.0 CD2 E:LEU468 4.5 36.9 1.0 CG E:ASP467 4.5 42.0 1.0 O E:ASP473 4.5 31.6 1.0 OD1 E:ASP473 4.6 44.0 1.0 O E:HOH1003 4.8 35.7 1.0 CB E:ASP467 4.9 34.2 1.0 CA E:ASP473 4.9 33.0 1.0 CB E:ASP172 4.9 38.3 1.0 O E:ASP467 4.9 42.4 1.0 CB E:ASP473 5.0 41.4 1.0

P.Gade, C.Chang, D.S.Pryde, D.Fletcher, S.Niven, L.G.Magalhaes, D.Robinson, J.Saini, P.E.Ibrahim, B.Forte, J.Wower, M.J.Bodkin, B.Baragana, I.H.Gilbert, K.Michalska, A.Joachimiak. Different Chemical Scaffolds Bind to L-Phe Site in Mycobacterium Tuberculosis Phe-Trna Synthetase Eur.J.Med.Chem. 17335 2025.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2025.117335