Magnesium in PDB 6dlj: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Nitro-Phenyldiketoacid

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

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Nitro-Phenyldiketoacid, PDB code: 6dlj 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)	49.89 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.759, 78.759, 224.475, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 25.9

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


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-Nitro-Phenyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:37.3 occ:1.00 O A:HOH920 2.0 39.2 1.0 OD1 A:ASP462 2.0 38.7 1.0 O06 A:GXM803 2.0 35.4 1.0 O A:HOH962 2.1 36.8 1.0 O08 A:GXM803 2.4 34.5 1.0 OE2 A:GLU434 2.5 38.4 1.0 C04 A:GXM803 2.9 37.8 1.0 C05 A:GXM803 2.9 38.5 1.0 CG A:ASP462 3.1 39.2 1.0 CD A:GLU434 3.5 40.2 1.0 CB A:ASP462 3.7 37.7 1.0 NH1 A:ARG339 3.8 40.1 1.0 OE1 A:GLU434 3.8 37.8 1.0 C03 A:GXM803 3.8 36.2 1.0 OD1 A:ASP274 3.9 41.3 1.0 O01 A:GXM803 4.0 37.3 1.0 O07 A:GXM803 4.1 37.6 1.0 CB A:ALA635 4.2 33.1 1.0 OD2 A:ASP462 4.2 38.1 1.0 NZ A:LYS399 4.2 37.7 1.0 OE1 A:GLU273 4.3 39.3 1.0 C02 A:GXM803 4.5 37.7 1.0 CG A:ASP274 4.7 42.8 1.0 CZ A:ARG339 4.7 35.4 1.0 N A:ASP462 4.7 36.9 1.0 CA A:ASP462 4.7 37.3 1.0 CG A:GLU434 4.8 40.7 1.0 CE A:MET432 4.9 38.5 1.0 NH2 A:ARG339 4.9 32.2 1.0 CB A:ASP274 5.0 34.5 1.0

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


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-Nitro-Phenyldiketoacid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:62.4 occ:1.00 O A:HOH1000 2.2 39.3 1.0 NE2 A:HIS235 2.5 49.9 1.0 O A:HOH905 2.5 44.1 1.0 O A:HOH946 2.9 61.0 1.0 OD1 A:ASN234 3.0 51.8 1.0 CE1 A:HIS235 3.0 50.6 1.0 CD2 A:HIS235 3.4 53.8 1.0 ND1 A:HIS235 4.0 51.0 1.0 CG A:ASN234 4.0 50.5 1.0 CG A:HIS235 4.2 48.3 1.0 ND2 A:ASN234 4.3 49.0 1.0 O A:HIS556 4.7 44.6 1.0 O A:SER179 4.8 50.3 1.0 NE2 A:GLN216 5.0 57.4 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