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Magnesium in PDB 2gq3: Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A

Enzymatic activity of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A

All present enzymatic activity of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A:
2.3.3.9;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A, PDB code: 2gq3 was solved by D.M.Anstrom, S.J.Remington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.380, 120.380, 238.889, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A (pdb code 2gq3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A, PDB code: 2gq3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2gq3

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Magnesium binding site 1 out of 4 in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1000

b:24.1
occ:1.00
 OD1 A:ASP462 2.0 36.7 1.0
O A:HOH2651 2.1 21.5 1.0
O1 A:MLT900 2.1 19.6 1.0
O3 A:MLT900 2.1 22.4 1.0
OE1 A:GLU434 2.1 37.5 1.0
O A:HOH2652 2.2 18.1 1.0
C1 A:MLT900 2.8 23.6 1.0
CG A:ASP462 2.9 37.5 1.0
C2 A:MLT900 3.1 24.4 1.0
CD A:GLU434 3.1 38.1 1.0
CB A:ASP462 3.3 34.4 1.0
OE2 A:GLU434 3.5 39.7 1.0
O4 A:MLT900 3.8 41.6 1.0
C3 A:MLT900 4.0 39.6 1.0
O2 A:MLT900 4.0 21.2 1.0
OD2 A:ASP462 4.1 35.2 1.0
NH1 A:ARG339 4.1 41.0 1.0
OD1 A:ASP274 4.2 44.6 1.0
NZ A:LYS399 4.2 43.1 1.0
CB A:ALA635 4.3 39.1 1.0
N A:ASP462 4.3 36.8 1.0
C4 A:MLT900 4.4 43.8 1.0
CG A:GLU434 4.4 35.5 1.0
CA A:ASP462 4.4 36.9 1.0
CB A:GLU434 4.7 37.1 1.0
OE1 A:GLU273 4.7 39.5 1.0
CE A:MET432 4.8 33.2 1.0
CA A:GLY459 4.8 37.4 1.0
O A:GLY459 4.9 39.2 1.0
CG A:ASP274 5.0 42.0 1.0

Magnesium binding site 2 out of 4 in 2gq3

Go back to Magnesium Binding Sites List in 2gq3
Magnesium binding site 2 out of 4 in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:40.9
occ:1.00
 O A:HOH2801 1.7 47.2 1.0
O A:LYS377 2.0 39.6 1.0
O A:LEU385 2.3 46.5 1.0
O A:HIS374 2.3 38.0 1.0
O A:GLY383 2.8 39.8 1.0
O A:ASN382 3.1 41.3 1.0
C A:LYS377 3.1 40.8 1.0
C A:LEU385 3.4 45.0 1.0
C A:HIS374 3.5 36.7 1.0
C A:GLY383 3.7 41.7 1.0
C A:ASN382 3.7 41.7 1.0
O A:ASN295 3.7 38.7 1.0
CB A:ASN382 3.8 42.4 1.0
N A:LEU385 3.8 44.1 1.0
CA A:ALA378 3.9 42.4 1.0
N A:ALA378 3.9 41.6 1.0
CA A:GLY375 4.0 38.4 1.0
CA A:LEU385 4.1 45.0 1.0
N A:LYS377 4.2 39.7 1.0
C A:PRO384 4.2 44.4 1.0
CA A:LYS377 4.2 42.2 1.0
N A:GLY375 4.3 36.9 1.0
N A:GLY383 4.4 41.3 1.0
CA A:GLY383 4.4 40.8 1.0
CA A:ASN382 4.4 41.7 1.0
CA A:HIS374 4.5 36.3 1.0
C A:GLY375 4.5 39.1 1.0
N A:ILE386 4.5 44.6 1.0
N A:PRO384 4.5 42.7 1.0
O A:PRO384 4.6 46.2 1.0
CB A:LEU385 4.7 45.5 1.0
O A:LYS296 4.7 43.3 1.0
CB A:HIS374 4.8 36.7 1.0
CB A:ALA378 4.8 41.6 1.0
N A:SER379 4.8 42.2 1.0
CA A:PRO384 4.8 43.3 1.0
CA A:LYS296 4.8 41.0 1.0
N A:LEU376 4.8 38.6 1.0
C A:ALA378 4.8 42.8 1.0
CG1 A:ILE386 4.9 42.3 1.0
C A:ASN295 4.9 39.3 1.0
CA A:ILE386 4.9 43.8 1.0

Magnesium binding site 3 out of 4 in 2gq3

Go back to Magnesium Binding Sites List in 2gq3
Magnesium binding site 3 out of 4 in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:37.0
occ:1.00
 O3 B:MLT901 1.9 36.5 1.0
O B:HOH2654 2.0 44.6 1.0
OD1 B:ASP462 2.0 39.3 1.0
O1 B:MLT901 2.1 29.6 1.0
OE1 B:GLU434 2.1 39.4 1.0
O B:HOH2653 2.4 35.3 1.0
C1 B:MLT901 2.8 37.5 1.0
C2 B:MLT901 3.0 38.2 1.0
CG B:ASP462 3.1 40.3 1.0
CD B:GLU434 3.2 39.5 1.0
OE2 B:GLU434 3.6 40.0 1.0
CB B:ASP462 3.6 38.4 1.0
O4 B:MLT901 3.7 45.0 1.0
C3 B:MLT901 3.9 45.1 1.0
OD1 B:ASP274 3.9 42.7 1.0
NZ B:LYS399 4.0 37.4 1.0
NH1 B:ARG339 4.1 39.3 1.0
O2 B:MLT901 4.1 32.2 1.0
C4 B:MLT901 4.1 49.1 1.0
OD2 B:ASP462 4.2 35.8 1.0
OE1 B:GLU273 4.3 30.4 1.0
CG B:GLU434 4.4 38.9 1.0
CB B:ALA635 4.6 38.2 1.0
CG B:ASP274 4.6 41.8 1.0
N B:ASP462 4.7 37.9 1.0
CB B:GLU434 4.7 38.4 1.0
CA B:ASP462 4.8 38.4 1.0
CE B:MET432 4.8 33.9 1.0
OE2 B:GLU273 4.9 31.5 1.0
CZ B:ARG339 5.0 37.3 1.0

Magnesium binding site 4 out of 4 in 2gq3

Go back to Magnesium Binding Sites List in 2gq3
Magnesium binding site 4 out of 4 in the Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mycobacterium Tuberculosis Malate Synthase in Complex with Magnesium, Malate, and Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1003

b:76.6
occ:1.00
 O B:LYS377 2.1 46.3 1.0
O B:HIS374 2.1 39.1 1.0
O B:HOH2802 2.2 57.5 1.0
O B:LEU385 2.5 42.5 1.0
O B:ASN382 2.7 49.9 1.0
O B:GLY383 2.9 45.2 1.0
C B:HIS374 3.3 38.4 1.0
C B:LYS377 3.3 45.7 1.0
C B:ASN382 3.4 48.5 1.0
CB B:ASN382 3.5 49.0 1.0
C B:GLY383 3.6 45.9 1.0
C B:LEU385 3.6 43.1 1.0
O B:ASN295 3.6 36.3 1.0
N B:LEU385 3.9 44.5 1.0
CA B:ASN382 4.1 48.9 1.0
CA B:ALA378 4.1 46.9 1.0
N B:ALA378 4.1 46.8 1.0
C B:PRO384 4.1 44.6 1.0
N B:GLY375 4.2 37.5 1.0
N B:GLY383 4.2 47.8 1.0
CA B:GLY375 4.2 37.3 1.0
CA B:LEU385 4.2 43.4 1.0
CA B:HIS374 4.2 38.4 1.0
N B:LYS377 4.2 43.5 1.0
CA B:GLY383 4.3 46.6 1.0
N B:PRO384 4.3 45.7 1.0
CA B:LYS377 4.3 45.2 1.0
CA B:PRO384 4.5 45.3 1.0
O B:PRO384 4.5 44.4 1.0
CB B:HIS374 4.6 37.7 1.0
C B:GLY375 4.6 37.1 1.0
CG B:ASN382 4.7 49.1 1.0
N B:ILE386 4.7 42.2 1.0
O B:LYS296 4.8 38.7 1.0
C B:ASN295 4.8 37.0 1.0
CA B:LYS296 4.8 35.6 1.0
CB B:LEU385 4.8 43.6 1.0
N B:SER379 4.8 48.1 1.0
C B:LYS296 5.0 35.9 1.0
C B:ALA378 5.0 47.6 1.0

Reference:

D.M.Anstrom, S.J.Remington. The Product Complex of M. Tuberculosis Malate Synthase Revisited. Protein Sci. V. 15 2002 2006.
ISSN: ISSN 0961-8368
PubMed: 16877713
DOI: 10.1110/PS.062300206
Page generated: Mon Dec 14 07:24:48 2020

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