Magnesium in PDB 5h8u: Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate:
2.3.3.9;

The structure of Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate, PDB code: 5h8u was solved by I.V.Krieger, H.-L.Huang, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.36 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.659, 120.659, 232.224, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.6

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate (pdb code 5h8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate, PDB code: 5h8u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate


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 Wild-Type Malate Synthase in Complex with Product Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:76.6 occ:1.00 O A:HOH917 2.0 74.7 1.0 O2 A:LMR802 2.0 78.2 1.0 O4A A:LMR802 2.2 88.4 1.0 OD2 A:ASP462 2.3 90.2 1.0 OE1 A:GLU434 2.5 60.9 1.0 C3 A:LMR802 2.8 73.0 1.0 C4 A:LMR802 2.9 98.9 1.0 C2 A:LMR802 2.9 67.5 1.0 CG A:ASP462 3.3 96.9 1.0 CD A:GLU434 3.4 65.9 1.0 OE2 A:GLU434 3.5 73.9 1.0 OD1 A:ASP274 3.8 95.2 1.0 CB A:ASP462 4.0 87.1 1.0 NH1 A:ARG339 4.0 67.8 1.0 O4B A:LMR802 4.0 93.9 1.0 NZ A:LYS399 4.1 62.6 1.0 OD1 A:ASP462 4.1 75.4 1.0 C1 A:LMR802 4.2 78.9 1.0 OE2 A:GLU273 4.3 74.8 1.0 CG A:ASP274 4.4 81.2 1.0 O1B A:LMR802 4.6 70.1 1.0 CE A:MET432 4.6 60.5 1.0 CG A:GLU434 4.7 68.1 1.0 CZ A:ARG339 4.8 52.0 1.0 CB A:ALA635 4.9 78.9 1.0 OE1 A:GLU273 4.9 84.2 1.0 OD2 A:ASP274 5.0 82.0 1.0 CD A:GLU273 5.0 75.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate


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 Wild-Type Malate Synthase in Complex with Product Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:67.1 occ:1.00 OE2 B:GLU434 2.0 60.2 1.0 O1 B:GLV803 2.0 72.8 1.0 O3 B:GLV803 2.1 56.9 1.0 O B:HOH903 2.1 79.0 1.0 O B:HOH917 2.2 78.5 1.0 C1 B:GLV803 2.6 62.3 1.0 C2 B:GLV803 2.6 65.1 1.0 OD2 B:ASP462 2.7 74.0 1.0 CD B:GLU434 3.0 69.2 1.0 OE1 B:GLU434 3.4 69.4 1.0 CG B:ASP462 3.5 71.6 1.0 CB B:ASP462 3.6 61.6 1.0 OD2 B:ASP274 3.8 92.9 1.0 O2 B:GLV803 3.8 72.8 1.0 CE B:MET432 4.0 75.5 1.0 NH1 B:ARG339 4.1 71.6 1.0 CG B:GLU434 4.3 62.4 1.0 CB B:GLU434 4.5 55.8 1.0 N B:ASP462 4.6 47.3 1.0 OD1 B:ASP462 4.7 79.1 1.0 CA B:GLY459 4.7 67.2 1.0 NZ B:LYS399 4.7 65.6 1.0 CA B:ASP462 4.8 46.9 1.0 CB B:ALA635 4.9 66.3 1.0 CG B:ASP274 5.0 92.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Wild-Type Malate Synthase in Complex with Product Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:55.5 occ:1.00 O B:HOH920 2.2 71.1 1.0 NH2 B:ARG69 2.2 87.8 1.0 CZ B:ARG69 3.4 88.3 1.0 CD B:ARG69 4.2 93.1 1.0 NE B:ARG69 4.2 94.2 1.0 NZ B:LYS66 4.2 98.0 1.0 NH1 B:ARG69 4.3 83.2 1.0 CG B:LYS66 4.6 76.2 1.0 NH2 B:ARG70 5.0 82.9 1.0

H.L.Huang, I.V.Krieger, M.K.Parai, V.B.Gawandi, J.C.Sacchettini. Mycobacterium Tuberculosis Malate Synthase Structures with Fragments Reveal A Portal For Substrate/Product Exchange. J. Biol. Chem. V. 291 27421 2016.
ISSN: ESSN 1083-351X
PubMed: 27738104
DOI: 10.1074/JBC.M116.750877