Magnesium in PDB 6axb: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Naphthyldiketoacid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Naphthyldiketoacid:
2.3.3.9;

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Naphthyldiketoacid, PDB code: 6axb 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)	45.15 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.941, 79.941, 225.146, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Naphthyldiketoacid (pdb code 6axb). 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 2-Naphthyldiketoacid, PDB code: 6axb:
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 2-Naphthyldiketoacid


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 2-Naphthyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:25.0 occ:1.00 OD1 A:ASP462 2.0 21.0 1.0 O05 A:C0V802 2.1 24.9 0.9 OE2 A:GLU434 2.1 21.0 1.0 O A:HOH1057 2.2 19.3 1.0 O A:HOH936 2.2 22.0 1.0 O01 A:C0V802 2.3 22.4 0.8 C04 A:C0V802 2.8 25.5 1.0 C02 A:C0V802 2.9 22.7 1.0 CG A:ASP462 3.0 24.0 1.0 CD A:GLU434 3.1 24.2 1.0 CB A:ASP462 3.5 17.4 1.0 OE1 A:GLU434 3.5 22.0 1.0 NH1 A:ARG339 4.0 18.5 1.0 C06 A:C0V802 4.1 23.3 1.0 NZ A:LYS399 4.1 22.8 1.0 OD1 A:ASP274 4.1 27.8 1.0 OD2 A:ASP462 4.1 21.2 1.0 O08 A:C0V802 4.2 27.0 0.8 O03 A:C0V802 4.2 20.3 1.0 CG A:GLU434 4.3 17.8 1.0 CB A:ALA635 4.3 18.2 1.0 OE1 A:GLU273 4.5 19.4 1.0 N A:ASP462 4.5 20.1 1.0 CB A:GLU434 4.6 20.2 1.0 CA A:ASP462 4.6 19.7 1.0 C07 A:C0V802 4.6 28.1 1.0 CG A:ASP274 4.9 24.6 1.0 CE A:MET432 4.9 20.7 1.0 CA A:GLY459 5.0 18.3 1.0 O A:GLY459 5.0 19.5 1.0

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


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 2-Naphthyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg806 b:39.3 occ:1.00 O A:HOH1085 1.9 38.9 1.0 O A:HOH1256 2.0 37.5 1.0 O A:HOH1325 2.0 40.9 1.0 O A:HOH1438 2.2 38.7 1.0 NE2 A:HIS235 2.3 31.3 1.0 O A:HOH1091 2.3 38.3 1.0 CE1 A:HIS235 3.1 35.5 1.0 CD2 A:HIS235 3.4 31.8 1.0 O A:HOH1180 4.0 41.1 1.0 ND1 A:HIS235 4.3 24.8 1.0 CB A:ASP559 4.4 31.8 1.0 CG A:HIS235 4.4 30.6 1.0 OD1 A:ASN234 4.5 31.6 1.0 OD2 A:ASP559 4.5 31.3 1.0 O A:HOH1302 4.5 48.1 1.0 CG A:ASP559 4.8 32.7 1.0 O A:HOH1346 5.0 47.9 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