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Magnesium in PDB 3s9i: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor, PDB code: 3s9i was solved by I.V.Krieger, Q.Sun, J.C.Sacchettini, Mycobacterium Tuberculosisstructural Proteomics Project (Xmtb), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.99 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.331, 79.331, 225.945, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor (pdb code 3s9i). 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 Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor, PDB code: 3s9i:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3s9i

Go back to Magnesium Binding Sites List in 3s9i
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor


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 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg743

b:19.2
occ:1.00
 OE2 A:GLU434 1.9 15.2 1.0
O A:HOH1253 2.1 17.4 1.0
O8 A:XI7742 2.1 23.1 1.0
OD1 A:ASP462 2.1 17.6 1.0
O A:HOH1252 2.1 23.7 1.0
O11 A:XI7742 2.2 19.0 1.0
C9 A:XI7742 2.9 24.9 1.0
CD A:GLU434 2.9 23.7 1.0
C10 A:XI7742 3.0 20.8 1.0
CG A:ASP462 3.1 20.9 1.0
OE1 A:GLU434 3.4 18.2 1.0
CB A:ASP462 3.5 14.3 1.0
NH1 A:ARG339 4.0 21.3 1.0
OD1 A:ASP274 4.1 33.2 1.0
O10 A:XI7742 4.2 18.8 1.0
C8 A:XI7742 4.2 30.5 1.0
O14 A:XI7742 4.2 37.0 1.0
NZ A:LYS399 4.2 29.8 1.0
CG A:GLU434 4.2 17.9 1.0
OD2 A:ASP462 4.3 18.4 1.0
CB A:ALA635 4.4 18.7 1.0
N A:ASP462 4.5 14.0 1.0
CB A:GLU434 4.5 13.9 1.0
CA A:ASP462 4.6 12.6 1.0
OE1 A:GLU273 4.6 27.2 1.0
C7 A:XI7742 4.7 35.3 1.0
CE A:MET432 4.7 17.2 1.0
CA A:GLY459 4.8 13.5 1.0
CG A:ASP274 4.9 32.0 1.0
O A:GLY459 4.9 12.9 1.0

Magnesium binding site 2 out of 3 in 3s9i

Go back to Magnesium Binding Sites List in 3s9i
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor


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 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg744

b:31.6
occ:1.00
 O A:HOH1323 2.0 30.8 1.0
O A:HOH1325 2.0 28.2 1.0
O A:HOH1327 2.1 31.6 1.0
O A:HOH1326 2.1 36.9 1.0
O A:HOH964 2.1 33.4 1.0
O A:HOH1324 2.1 30.5 1.0
O A:HOH1353 4.0 31.2 1.0
OD1 A:ASP65 4.1 33.1 1.0
O A:HOH931 4.2 28.8 1.0
OE1 A:GLN704 4.2 32.4 1.0
NH1 A:ARG69 4.3 26.7 1.0
O A:HOH936 4.5 40.6 1.0
O A:HOH975 4.6 29.0 1.0
NE2 A:GLN704 4.7 32.8 1.0
O A:HOH748 4.7 45.4 1.0
NH2 A:ARG69 4.9 24.4 1.0
CD A:GLN704 4.9 39.8 1.0
CZ A:ARG69 5.0 36.7 1.0

Magnesium binding site 3 out of 3 in 3s9i

Go back to Magnesium Binding Sites List in 3s9i
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor


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 Malate Synthase in Complex with 2-4-Dioxo-4-Phenylbutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg745

b:33.6
occ:1.00
 O A:HOH1365 1.9 44.6 1.0
O A:HOH1334 2.0 42.5 1.0
O A:HOH1364 2.1 46.4 1.0
NE2 A:HIS235 2.1 23.2 1.0
O A:HOH1336 2.2 33.2 1.0
O A:HOH1339 2.3 44.6 1.0
CE1 A:HIS235 3.1 23.1 1.0
CD2 A:HIS235 3.2 23.7 1.0
ND1 A:HIS235 4.2 22.9 1.0
OD2 A:ASP559 4.3 38.2 1.0
CG A:HIS235 4.3 21.7 1.0
CB A:ASP559 4.4 21.2 1.0
OD1 A:ASN234 4.5 23.5 1.0
O A:HOH1269 4.5 39.9 1.0
O A:HOH1072 4.6 44.2 1.0
CG A:ASP559 4.6 31.2 1.0
O A:HOH1197 4.9 71.7 1.0

Reference:

I.V.Krieger, J.S.Freundlich, V.B.Gawandi, J.P.Roberts, V.B.Gawandi, Q.Sun, J.L.Owen, M.T.Fraile, S.I.Huss, J.L.Lavandera, T.R.Ioerger, J.C.Sacchettini. Structure-Guided Discovery of Phenyl-Diketo Acids As Potent Inhibitors of M. Tuberculosis Malate Synthase. Chem.Biol. V. 19 1556 2012.
ISSN: ISSN 1074-5521
PubMed: 23261599
DOI: 10.1016/J.CHEMBIOL.2012.09.018
Page generated: Mon Dec 14 08:50:01 2020

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