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Magnesium in PDB 3sb0: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor, PDB code: 3sb0 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) 45.61 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.534, 78.534, 224.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.3

Other elements in 3sb0:

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor (pdb code 3sb0). 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 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor, PDB code: 3sb0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3sb0

Go back to Magnesium Binding Sites List in 3sb0
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic 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 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:30.1
occ:1.00
 OE2 A:GLU434 2.2 28.0 1.0
OD1 A:ASP462 2.2 29.4 1.0
O A:HOH902 2.2 31.0 1.0
O12 A:I93802 2.2 28.3 1.0
O15 A:I93802 2.3 25.0 1.0
O A:HOH901 2.4 27.7 1.0
C11 A:I93802 2.9 28.9 0.8
C13 A:I93802 2.9 24.9 0.9
CG A:ASP462 3.2 28.2 1.0
CD A:GLU434 3.2 26.5 1.0
CB A:ASP462 3.6 23.9 1.0
OE1 A:GLU434 3.6 25.9 1.0
C10 A:I93802 4.0 26.8 1.0
NH1 A:ARG339 4.0 30.2 1.0
O09 A:I93802 4.1 29.0 0.8
O14 A:I93802 4.2 25.2 0.8
OD2 A:ASP462 4.3 29.0 1.0
NZ A:LYS399 4.3 25.7 1.0
CB A:ALA635 4.3 27.2 1.0
OD1 A:ASP274 4.3 25.7 1.0
CG A:GLU434 4.4 22.7 1.0
N A:ASP462 4.5 25.9 1.0
C08 A:I93802 4.6 29.9 0.9
CA A:ASP462 4.6 23.6 1.0
CB A:GLU434 4.6 21.0 1.0
CE A:MET432 4.7 26.0 1.0
OE1 A:GLU273 4.8 32.0 1.0
CA A:GLY459 4.8 23.5 1.0
CZ A:ARG339 5.0 26.4 1.0
O A:GLY459 5.0 24.1 1.0

Magnesium binding site 2 out of 3 in 3sb0

Go back to Magnesium Binding Sites List in 3sb0
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic 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 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:43.1
occ:1.00
 O A:HOH1258 2.2 34.2 1.0
O A:HOH1260 2.3 40.8 1.0
O A:HOH1257 2.3 35.1 1.0
O A:HOH1279 2.3 39.6 1.0
O A:HOH1254 2.5 37.6 1.0
O A:HOH1287 2.7 52.4 1.0
O A:HOH1068 3.8 35.5 1.0
O A:HOH911 3.9 30.4 1.0
O A:HOH1224 4.1 41.8 1.0
O A:ALA703 4.2 32.4 1.0
OD1 A:ASP65 4.4 39.5 1.0
O A:GLN704 4.5 33.6 1.0
NE2 A:HIS469 4.6 28.1 1.0
C A:GLN704 4.8 30.9 1.0
CG A:GLN61 4.9 27.4 1.0
O A:GLN705 4.9 27.8 1.0
O A:HOH1069 4.9 35.2 1.0
CA A:GLN704 4.9 30.0 1.0
O A:HOH941 4.9 29.8 1.0

Magnesium binding site 3 out of 3 in 3sb0

Go back to Magnesium Binding Sites List in 3sb0
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic 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 4-(2-Chloro-6-Fluoro-3-Methylphenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:45.4
occ:1.00
 O A:HOH1298 2.3 40.8 1.0
O A:HOH1294 2.4 42.1 1.0
O A:HOH1300 2.5 46.2 1.0
NE2 A:HIS235 2.5 32.1 1.0
O A:HOH1266 2.5 45.2 1.0
O A:HOH1297 2.8 48.1 1.0
CE1 A:HIS235 3.3 30.1 1.0
CD2 A:HIS235 3.5 30.5 1.0
OD1 A:ASN234 4.2 28.8 1.0
O A:HOH1221 4.2 46.3 1.0
ND1 A:HIS235 4.5 30.6 1.0
CG A:HIS235 4.6 30.4 1.0
OD2 A:ASP559 4.7 46.1 1.0
CB A:ASP559 4.9 33.9 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: Thu Aug 15 10:50:20 2024

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