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Magnesium in PDB 5drc: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid, PDB code: 5drc was solved by 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) 44.78 / 2.18
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.957, 78.957, 224.974, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid (pdb code 5drc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid, PDB code: 5drc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5drc

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid


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-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:11.2
occ:1.00
 OD2 A:ASP462 2.0 16.6 1.0
OE2 A:GLU434 2.1 12.4 1.0
O05 A:5ER805 2.1 15.9 1.0
O A:HOH1022 2.2 12.1 1.0
O A:HOH978 2.2 12.7 1.0
O03 A:5ER805 2.2 14.0 1.0
C04 A:5ER805 2.8 17.7 1.0
C02 A:5ER805 2.9 14.3 1.0
CG A:ASP462 3.1 16.6 1.0
CD A:GLU434 3.1 18.1 1.0
OE1 A:GLU434 3.4 14.0 1.0
CB A:ASP462 3.6 14.0 1.0
NH1 A:ARG339 4.0 13.7 1.0
C06 A:5ER805 4.1 18.0 1.0
OD1 A:ASP462 4.1 17.4 1.0
O01 A:5ER805 4.2 12.8 1.0
NZ A:LYS399 4.2 13.3 1.0
OD2 A:ASP274 4.2 19.1 1.0
O08 A:5ER805 4.3 25.1 1.0
CG A:GLU434 4.4 9.7 1.0
CB A:ALA635 4.4 13.8 1.0
OE1 A:GLU273 4.5 12.3 1.0
N A:ASP462 4.6 15.0 1.0
C07 A:5ER805 4.6 27.2 1.0
CB A:GLU434 4.6 14.1 1.0
CA A:ASP462 4.7 13.8 1.0
CE A:MET432 4.8 10.5 1.0
CA A:GLY459 4.9 13.8 1.0
O A:GLY459 4.9 13.4 1.0
CG A:ASP274 4.9 17.6 1.0

Magnesium binding site 2 out of 4 in 5drc

Go back to Magnesium Binding Sites List in 5drc
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid


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-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.4
occ:1.00
 O A:HOH1151 2.1 24.1 1.0
O A:HOH1155 2.3 21.3 1.0
O A:HOH1259 2.5 27.0 1.0
O A:HOH1149 2.8 23.4 1.0
O A:HOH1194 4.0 28.8 1.0
OD1 A:ASP58 4.3 33.4 1.0
NE2 A:HIS469 4.3 14.2 1.0
O A:GLN705 4.4 14.8 1.0
O A:HOH917 4.4 27.6 1.0
CA A:PRO706 4.6 15.1 1.0
O A:HOH1160 4.6 21.9 1.0
O A:GLN704 4.7 23.2 1.0
CG A:GLN61 4.7 13.5 1.0
O A:ALA703 4.8 16.9 1.0
C A:GLN705 4.8 17.9 1.0
CE1 A:HIS469 4.8 16.1 1.0
N A:PRO706 4.9 18.3 1.0
C A:GLN704 4.9 18.7 1.0
N A:ASN707 5.0 16.1 1.0

Magnesium binding site 3 out of 4 in 5drc

Go back to Magnesium Binding Sites List in 5drc
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid


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-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:28.6
occ:1.00
 O A:HOH934 1.9 29.7 1.0
OE1 A:GLU87 2.0 30.8 1.0
O01 A:5ER806 2.1 25.9 1.0
O05 A:5ER806 2.2 24.0 1.0
C02 A:5ER806 2.8 29.2 1.0
C04 A:5ER806 2.9 24.8 1.0
CD A:GLU87 3.0 27.7 1.0
OE2 A:GLU87 3.3 31.3 1.0
O A:HOH901 3.4 23.0 1.0
O03 A:5ER806 4.1 22.7 1.0
C06 A:5ER806 4.2 23.4 1.0
CG A:GLU87 4.4 27.6 1.0
OE1 A:GLN83 4.7 38.8 1.0
O08 A:5ER806 4.9 25.8 1.0

Magnesium binding site 4 out of 4 in 5drc

Go back to Magnesium Binding Sites List in 5drc
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Hydroxy-4-(1H-Indol-3-Yl)-4-Oxobut-2-Enoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:12.4
occ:1.00
 OG1 A:THR482 3.1 25.4 1.0
NE1 A:TRP589 3.2 30.6 1.0
N A:ARG479 3.4 19.3 1.0
CG A:ARG479 3.6 27.0 1.0
CB A:VAL478 3.7 17.8 1.0
O A:HOH1286 3.8 38.6 1.0
CB A:THR482 3.8 18.9 1.0
CD A:ARG479 3.9 22.9 1.0
CA A:VAL478 3.9 16.4 1.0
CB A:ARG479 4.0 19.9 1.0
CG2 A:THR482 4.0 17.1 1.0
CE2 A:TRP589 4.1 25.3 1.0
CG1 A:VAL478 4.1 13.9 1.0
C A:VAL478 4.2 17.5 1.0
CD1 A:TRP589 4.2 32.1 1.0
CZ2 A:TRP589 4.3 24.1 1.0
CA A:ARG479 4.3 21.7 1.0
CG2 A:VAL478 4.9 15.0 1.0

Reference:

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
Page generated: Sun Sep 29 02:58:11 2024

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