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Magnesium in PDB 3s9z: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor

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

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Bromophenyl)-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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor, PDB code: 3s9z 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) 45.05 / 1.79
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.452, 79.452, 226.263, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.9

Other elements in 3s9z:

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

Bromine (Br) 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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor (pdb code 3s9z). 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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor, PDB code: 3s9z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3s9z

Go back to Magnesium Binding Sites List in 3s9z
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Bromophenyl)-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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:34.7
occ:1.00
 NE2 A:HIS235 2.3 25.5 1.0
O A:HOH1559 2.4 34.6 1.0
O A:HOH1650 2.4 49.4 1.0
O A:HOH1651 2.5 45.0 1.0
O A:HOH1623 2.5 46.1 1.0
O A:HOH1537 2.6 41.5 1.0
CE1 A:HIS235 3.2 30.3 1.0
CD2 A:HIS235 3.3 35.0 1.0
O A:HOH1593 4.3 64.7 1.0
ND1 A:HIS235 4.3 22.8 1.0
OD2 A:ASP559 4.4 33.8 1.0
CG A:HIS235 4.4 25.1 1.0
CB A:ASP559 4.5 28.6 1.0
O A:HOH1206 4.6 45.0 1.0
OD1 A:ASN234 4.7 25.5 1.0
CG A:ASP559 4.7 35.8 1.0
O A:HOH1427 4.8 42.8 1.0

Magnesium binding site 2 out of 3 in 3s9z

Go back to Magnesium Binding Sites List in 3s9z
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Bromophenyl)-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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.7
occ:1.00
 OE2 A:GLU434 2.1 15.7 1.0
OD1 A:ASP462 2.1 18.6 1.0
O A:HOH1534 2.2 18.7 1.0
O05 A:I92803 2.2 19.8 1.0
O A:HOH1533 2.3 20.7 1.0
O03 A:I92803 2.3 16.9 0.8
C04 A:I92803 2.7 20.3 0.9
C02 A:I92803 2.8 13.7 0.9
CD A:GLU434 3.0 19.7 1.0
CG A:ASP462 3.1 23.6 1.0
OE1 A:GLU434 3.4 19.3 1.0
CB A:ASP462 3.5 19.1 1.0
NH1 A:ARG339 3.9 19.2 1.0
C06 A:I92803 4.1 16.4 0.9
O01 A:I92803 4.2 13.5 0.9
NZ A:LYS399 4.2 21.3 1.0
OD2 A:ASP462 4.2 18.5 1.0
OD1 A:ASP274 4.2 22.4 1.0
CG A:GLU434 4.3 16.0 1.0
CB A:ALA635 4.4 21.3 1.0
O08 A:I92803 4.4 28.2 0.8
CB A:GLU434 4.6 18.7 1.0
N A:ASP462 4.6 17.6 1.0
OE1 A:GLU273 4.6 19.5 1.0
CA A:ASP462 4.6 16.3 1.0
C07 A:I92803 4.6 22.2 1.0
CE A:MET432 4.8 19.6 1.0
CA A:GLY459 4.9 16.3 1.0
CG A:ASP274 5.0 21.3 1.0
CZ A:ARG339 5.0 18.9 1.0

Magnesium binding site 3 out of 3 in 3s9z

Go back to Magnesium Binding Sites List in 3s9z
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 4-(2-Bromophenyl)-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-Bromophenyl)-2,4-Dioxobutanoic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:39.0
occ:1.00
 O A:HOH1624 2.2 30.5 1.0
O A:HOH1632 2.3 33.1 1.0
O A:HOH1633 2.4 33.2 1.0
O A:HOH1436 2.4 36.3 1.0
O A:HOH1626 2.5 40.5 1.0
O A:HOH1631 2.5 44.8 1.0
OD1 A:ASP65 4.1 30.8 1.0
O A:HOH1247 4.3 34.8 1.0
NH1 A:ARG69 4.3 31.4 1.0
OE1 A:GLN704 4.3 36.8 1.0
O A:HOH1619 4.4 38.6 1.0
NE2 A:GLN704 4.4 41.1 1.0
O A:HOH1191 4.4 25.9 1.0
CD A:GLN704 4.8 34.8 1.0
NH2 A:ARG69 4.9 30.5 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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