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Magnesium in PDB 3sad: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Mehtylphenyl)-2,4-Dioxobutanoic Acid Inhibitor

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Mehtylphenyl)-2,4-Dioxobutanoic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Mehtylphenyl)-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-Mehtylphenyl)-2,4-Dioxobutanoic Acid Inhibitor, PDB code: 3sad 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) 44.13 / 1.82
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.737, 77.737, 221.986, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 3sad

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

b:14.8
occ:1.00
 OD1 A:ASP462 2.1 11.2 1.0
O11 A:040802 2.2 13.2 1.0
OE2 A:GLU434 2.2 11.8 1.0
O A:HOH1428 2.2 12.4 1.0
O09 A:040802 2.3 14.7 1.0
O A:HOH1427 2.3 14.6 1.0
C07 A:040802 2.8 15.2 1.0
C08 A:040802 3.0 13.8 1.0
CG A:ASP462 3.1 12.8 1.0
CD A:GLU434 3.1 10.8 1.0
CB A:ASP462 3.5 14.6 1.0
OE1 A:GLU434 3.5 12.4 1.0
NH1 A:ARG339 3.9 9.8 1.0
NZ A:LYS399 4.0 11.9 1.0
C06 A:040802 4.1 13.8 1.0
O10 A:040802 4.1 12.0 1.0
OD1 A:ASP274 4.2 16.4 1.0
O05 A:040802 4.2 13.7 1.0
OD2 A:ASP462 4.2 13.4 1.0
CB A:ALA635 4.3 14.7 1.0
CG A:GLU434 4.4 11.6 1.0
OE1 A:GLU273 4.5 13.1 1.0
N A:ASP462 4.5 12.5 1.0
CA A:ASP462 4.6 11.2 1.0
C04 A:040802 4.6 17.4 1.0
CB A:GLU434 4.7 8.1 1.0
CE A:MET432 4.8 13.3 1.0
CZ A:ARG339 4.9 13.0 1.0
CG A:ASP274 4.9 15.6 1.0
CA A:GLY459 5.0 11.9 1.0

Magnesium binding site 2 out of 3 in 3sad

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

b:31.8
occ:1.00
 NE2 A:HIS235 2.3 17.4 1.0
O A:HOH1429 2.4 27.4 1.0
O A:HOH1431 2.4 31.4 1.0
O A:HOH1433 2.4 37.9 1.0
O A:HOH1432 2.4 31.6 1.0
O A:HOH1430 2.5 26.5 1.0
CD2 A:HIS235 3.2 21.7 1.0
CE1 A:HIS235 3.3 17.5 1.0
OD2 A:ASP559 4.3 20.0 1.0
OD1 A:ASN234 4.3 13.3 1.0
O A:HOH1200 4.3 30.1 1.0
CG A:HIS235 4.4 17.4 1.0
ND1 A:HIS235 4.4 16.0 1.0
CB A:ASP559 4.6 20.5 1.0
O A:HOH1251 4.6 37.7 1.0
CG A:ASP559 4.8 24.6 1.0
O A:HOH1285 4.8 40.0 1.0
O A:HOH989 4.9 23.3 1.0

Magnesium binding site 3 out of 3 in 3sad

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

b:36.1
occ:1.00
 O A:HOH1439 2.5 37.4 1.0
O A:HOH1218 2.5 27.7 1.0
O A:HOH1438 2.5 29.5 1.0
O A:HOH1440 2.5 37.4 1.0
O A:HOH1470 2.6 31.6 1.0
O A:HOH1346 2.7 40.0 1.0
O A:HOH1486 4.1 25.4 1.0
OD1 A:ASP65 4.2 19.3 1.0
NH1 A:ARG69 4.2 32.1 1.0
O A:HOH1197 4.4 26.3 1.0
O A:HOH1215 4.4 23.4 1.0
OE1 A:GLN704 4.5 34.4 1.0
O A:HOH1358 4.5 30.1 1.0
NE2 A:GLN704 4.7 30.0 1.0
NH2 A:ARG69 4.8 37.1 1.0
O A:HOH1475 4.8 30.9 1.0
CZ A:ARG69 4.9 34.7 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: Thu Aug 15 10:49:06 2024

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