Magnesium in PDB 1zvw: The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium

All present enzymatic activity of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium:
2.4.2.18;

The structure of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium, PDB code: 1zvw was solved by C.E.Lee, J.S.Lott, E.N.Baker, V.L.Arcus, F.Javid-Majd, C.Goodfellow, L.-W.Hung, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.417, 82.076, 118.873, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 25.5

The binding sites of Magnesium atom in the The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium (pdb code 1zvw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium, PDB code: 1zvw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4001 b:50.9 occ:1.00 O A:HOH6101 2.1 53.8 1.0 O3B A:PRP3966 2.1 66.2 1.0 O A:HOH6102 2.1 35.1 1.0 O1A A:PRP3966 2.2 68.1 1.0 OE1 A:GLU252 2.5 37.4 1.0 OG A:SER119 2.7 44.2 1.0 MG A:MG6001 3.1 55.8 1.0 PA A:PRP3966 3.3 67.3 1.0 PB A:PRP3966 3.3 67.7 1.0 CB A:SER119 3.4 40.5 1.0 O3A A:PRP3966 3.5 67.8 1.0 CD A:GLU252 3.5 39.5 1.0 OD2 A:ASP251 3.6 39.8 1.0 O A:HOH6115 3.8 46.5 1.0 OE2 A:GLU252 3.9 41.6 1.0 N A:GLY107 3.9 45.0 1.0 CA A:GLY107 4.0 48.9 1.0 O A:HOH6114 4.2 40.9 1.0 O4 A:PRP3966 4.2 71.0 1.0 O1B A:PRP3966 4.2 67.8 1.0 O A:HOH6123 4.3 56.9 1.0 CG A:ASP251 4.3 37.7 1.0 O1 A:PRP3966 4.3 70.3 1.0 O A:ASP251 4.4 35.8 1.0 O2A A:PRP3966 4.4 69.0 1.0 O2B A:PRP3966 4.4 68.2 1.0 N A:SER119 4.5 41.6 1.0 OD1 A:ASP251 4.5 41.7 1.0 CA A:SER119 4.5 41.1 1.0 C1 A:PRP3966 4.6 70.5 1.0 CG A:GLU252 4.7 36.9 1.0 C A:VAL106 4.8 41.3 1.0 C A:GLY107 4.9 50.7 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Trpd (RV2192C) From Mycobacterium Tuberculosis in Complex with Prpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg6001 b:55.8 occ:1.00 O A:HOH6117 2.1 57.8 1.0 OE1 A:GLU252 2.3 37.4 1.0 O A:HOH6123 2.4 56.9 1.0 OD1 A:ASP251 2.5 41.7 1.0 O A:HOH6101 2.5 53.8 1.0 O A:HOH6115 2.5 46.5 1.0 MG A:MG4001 3.1 50.9 1.0 CD A:GLU252 3.2 39.5 1.0 CG A:ASP251 3.2 37.7 1.0 OD2 A:ASP251 3.2 39.8 1.0 CG A:GLU252 3.4 36.9 1.0 OG1 A:THR115 3.6 70.1 1.0 O3B A:PRP3966 3.7 66.2 1.0 O A:ASP251 4.2 35.8 1.0 O A:HOH6102 4.3 35.1 1.0 OE2 A:GLU252 4.3 41.6 1.0 OD1 A:ASP111 4.4 67.5 1.0 C A:ASP251 4.5 37.4 1.0 O A:HOH6070 4.6 52.1 1.0 CB A:ASP251 4.6 37.9 1.0 OD2 A:ASP111 4.8 70.1 1.0 CB A:GLU252 4.8 37.0 1.0 PB A:PRP3966 4.8 67.7 1.0 CG A:ASP111 4.8 67.1 1.0 O1B A:PRP3966 4.9 67.8 1.0 CA A:ASP251 4.9 37.1 1.0 CB A:THR115 5.0 69.0 1.0 N A:ASP251 5.0 38.4 1.0

C.E.Lee, C.Goodfellow, F.Javid-Majd, E.N.Baker, J.S.Lott. The Crystal Structure of Trpd, A Metabolic Enzyme Essential For Lung Colonization By Mycobacterium Tuberculosis, in Complex with Its Substrate Phosphoribosylpyrophosphate. J.Mol.Biol. V. 355 784 2006.
ISSN: ISSN 0022-2836
PubMed: 16337227
DOI: 10.1016/J.JMB.2005.11.016