Magnesium in PDB 6c7b: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid:
2.3.3.9;

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid, PDB code: 6c7b was solved by I.V.Krieger, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 2.13
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.647, 78.647, 224.029, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.4

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid (pdb code 6c7b). 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 Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid, PDB code: 6c7b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:28.6 occ:1.00 OD1 A:ASP462 2.0 35.7 1.0 O A:HOH940 2.1 34.0 1.0 O A:HOH982 2.1 31.9 1.0 OE2 A:GLU434 2.1 31.0 1.0 O17 A:ENY801 2.2 32.0 1.0 O14 A:ENY801 2.3 33.2 1.0 C15 A:ENY801 2.9 32.2 1.0 CG A:ASP462 3.0 33.5 1.0 C13 A:ENY801 3.1 35.1 1.0 CD A:GLU434 3.2 31.8 1.0 CB A:ASP462 3.5 28.1 1.0 OE1 A:GLU434 3.7 30.8 1.0 O18 A:ENY801 4.1 38.3 1.0 C12 A:ENY801 4.1 35.5 1.0 OD2 A:ASP462 4.1 30.6 1.0 NH1 A:ARG339 4.2 33.2 1.0 O16 A:ENY801 4.2 30.2 1.0 OD1 A:ASP274 4.2 39.2 1.0 CB A:ALA635 4.4 32.1 1.0 NZ A:LYS399 4.4 41.2 1.0 N A:ASP462 4.5 30.4 1.0 CG A:GLU434 4.5 33.3 1.0 CA A:ASP462 4.6 32.6 1.0 OE1 A:GLU273 4.6 35.5 1.0 C11 A:ENY801 4.7 41.8 1.0 CB A:GLU434 4.7 31.1 1.0 CE A:MET432 4.8 26.1 1.0 O A:GLY459 4.9 31.9 1.0 CG A:ASP274 5.0 36.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid


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 Mycobacterium Tuberculosis Malate Synthase in Complex with Methoxynaphthyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:47.2 occ:1.00 O A:HOH953 1.9 49.9 1.0 O A:HOH1117 2.2 55.9 1.0 O A:HOH1101 2.3 47.1 1.0 O A:HOH1061 2.4 47.5 1.0 NE2 A:HIS235 2.5 39.9 1.0 O A:HOH1031 2.5 50.6 1.0 CE1 A:HIS235 3.2 37.4 1.0 CD2 A:HIS235 3.6 41.7 1.0 ND1 A:HIS235 4.4 39.6 1.0 OD1 A:ASN234 4.4 41.5 1.0 CG A:HIS235 4.6 38.2 1.0 CB A:ASP559 4.9 37.9 1.0 OD2 A:ASP559 4.9 41.9 1.0

J.F.Ellenbarger, I.V.Krieger, H.L.Huang, S.Gomez-Coca, T.R.Ioerger, J.C.Sacchettini, S.E.Wheeler, K.R.Dunbar. Anion-Pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase By Phenyl-Diketo Acids. J Chem Inf Model V. 58 2085 2018.
ISSN: ESSN 1549-960X
PubMed: 30137983
DOI: 10.1021/ACS.JCIM.8B00417