Magnesium in PDB 4zdk: Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine

All present enzymatic activity of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine:
6.3.4.2;

The structure of Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine, PDB code: 4zdk was solved by M.Bellinzoni, N.Barilone, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.68 / 3.49
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.732, 194.724, 207.457, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine (pdb code 4zdk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine, PDB code: 4zdk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine


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 the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:94.5 occ:1.00 OD2 A:ASP78 2.2 0.6 1.0 O3G A:ACP602 2.4 0.0 1.0 OE2 A:GLU152 2.7 0.6 1.0 CG A:ASP78 2.7 0.6 1.0 O1B A:ACP602 2.7 0.7 1.0 OD1 A:ASP78 2.7 0.0 1.0 OE1 A:GLU152 3.0 0.1 1.0 CD A:GLU152 3.2 0.6 1.0 CA A:GLY25 3.3 0.8 1.0 O1A A:ACP602 3.5 0.8 1.0 N A:GLY25 3.6 0.2 1.0 PB A:ACP602 3.6 0.9 1.0 PG A:ACP602 3.6 0.5 1.0 O2A A:ACP602 3.9 0.9 1.0 C3B A:ACP602 3.9 0.5 1.0 CB A:ASP78 4.0 0.5 1.0 NZ A:LYS46 4.0 0.8 1.0 PA A:ACP602 4.0 0.3 1.0 O3A A:ACP602 4.2 0.7 1.0 CE A:LYS46 4.3 0.1 1.0 O1G A:ACP602 4.4 1.0 1.0 CD A:LYS46 4.5 0.9 1.0 C A:GLY25 4.6 0.8 1.0 CG A:GLU152 4.7 0.5 1.0 C A:LYS24 4.8 0.7 1.0 O2G A:ACP602 4.8 0.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine


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 the M. Tuberculosis Ctp Synthase Pyrg in Complex with Utp, Amp-Pcp and Oxonorleucine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:0.3 occ:1.00 O1B B:ACP602 2.4 0.6 1.0 OD2 B:ASP78 2.6 0.7 1.0 OE2 B:GLU152 2.7 0.4 1.0 OD1 B:ASP78 3.0 0.3 1.0 O3A B:ACP602 3.0 0.1 1.0 CG B:ASP78 3.1 0.3 1.0 PB B:ACP602 3.1 0.7 1.0 OE1 B:GLU152 3.1 0.3 1.0 CA B:GLY25 3.1 0.3 1.0 CD B:GLU152 3.3 0.9 1.0 N B:GLY25 3.3 0.5 1.0 O1G B:ACP602 3.4 0.8 1.0 O3G B:ACP602 3.6 0.5 1.0 O1A B:ACP602 3.8 0.3 1.0 PG B:ACP602 3.8 0.8 1.0 C3B B:ACP602 4.0 0.5 1.0 PA B:ACP602 4.0 0.6 1.0 NZ B:LYS46 4.3 0.8 1.0 CB B:ASP78 4.3 0.4 1.0 C B:GLY25 4.4 0.4 1.0 O2B B:ACP602 4.5 0.9 1.0 C B:LYS24 4.6 0.8 1.0 CE B:LYS46 4.6 0.1 1.0 CG B:GLU152 4.8 0.6 1.0 CD B:LYS46 4.8 0.1 1.0 O5' B:ACP602 4.9 0.1 1.0 N B:LEU26 5.0 0.1 1.0

G.Mori, L.R.Chiarelli, M.Esposito, V.Makarov, M.Bellinzoni, R.C.Hartkoorn, G.Degiacomi, F.Boldrin, S.Ekins, A.L.De Jesus Lopes Ribeiro, L.B.Marino, I.Centarova, Z.Svetlikova, J.Blasko, E.Kazakova, A.Lepioshkin, N.Barilone, G.Zanoni, A.Porta, M.Fondi, R.Fani, A.R.Baulard, K.Mikusova, P.M.Alzari, R.Manganelli, L.P.De Carvalho, G.Riccardi, S.T.Cole, M.R.Pasca. Thiophenecarboxamide Derivatives Activated By Etha Kill Mycobacterium Tuberculosis By Inhibiting the Ctp Synthetase Pyrg. Chem.Biol. V. 22 917 2015.
ISSN: ISSN 1074-5521
PubMed: 26097035
DOI: 10.1016/J.CHEMBIOL.2015.05.016